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There was definitely track that ran Amtrak trains to Hyannis in the early 1990s. From what I know of the Cape - I spend most summers there - people would be delighted to have a railroad that really went somewhere again...
I'm pretty sure all the track you would need to do this is still in place if you aren't overly concerned with going fast. But some of that track is also track where the neighbors have a demonstrated habit of demonstrating against frequent train service.

I'm not sure to what extent anyone who would have to listen to demonstrators is in control of that; I would not be surprised if CSX currently owns the key pieces through Attleboro and Taunton that the demonstrators care about, and that track may or may not be included in the set of track that Massachusetts is not currently succeeding in buying from CSX. The railroad on Cape Cod probably doesn't have to give in to pressure from people in Attleboro and Taunton. And maybe if it was a few trains a day instead of a few trains an hour people would care less.

Though one other potential issue is that the state of Massachusetts may not be enthusiastic about subsidizing a train that Attleboro residents object to, and Amtrak isn't exactly known for agressively adding routes that states aren't contributing to.

And WAS to Hyannis might make a nice Acela route for service once every 3-4 hours if only there were electrification to Hyannis and enough Acela trainsets, even if the part north/east of Providence was on slower track.
 
One other issue that would come up with an NYP (or WAS) to Hyannis train is that there are a finite number of slots over the Connecticut River bridge. Stealing a slot from Shore Line East or a Boston-bound train is probably not good for the overall system.
 
More seriously, I see only upsides. Including LIRR passengers being able to connect directly with MetroNorth and 4 and 1 subway lines at GCT, and vice versa.
By the way, technically there are tracks that already connect the two stations. There's a shuttle NYC subway train that runs on them. I have no idea how much it would cost to replace them with Amtrak usable tracks, but at least the tunnel is already there.
One other potential issue is how close the stations are, what the relative elevations above/below sea level the existing tracks are, and whether a reasonable grade can connect them. There are probably ways to work this out, and maybe the details turn out to be such that this isn't a major problem, but I'm not sure.

(But GCT's headhouse appears to be roughly 2000 feet or maybe a bit more from the eastern tracks out of NYP; at a 3% grade, which may be more than the railroads might prefer, that only lets you have a 60' change in altitude. There's slop in all sorts of directions in my guesses here; I didn't measure all that precisely, and I don't know where the GCT tracks are relative to the GCT headhouse. But there may well not be enough room for the new NJT tracks to connect to tracks just below the street level at GCT without building a horribly indirect and therefore expensive tunnel, for example. Then again, connecting the upper levels at GCT to the upper levels at NYP and the lower levels at NYP to the lower levels at GCT might well work out just fine.)

I'm just feeling baffled that whether a GCT<->NYP track connection would be valuable is something that could be the subject of debate, which makes me suspect there must be some downside I'm missing. Or maybe people are just allergic to spending money on infrastructure?
While I'm not saying that it's impossible, connecting anything at GCT to NYP or the new NJT station isn't as simple as "let's dig a new tunnel. At GCT, there are loop tracks that run around all the stub end tracks. So you'd have to start by cutting those tracks, something that MN might not like.

Then you next have to deal with the fact that you've got the Lexington Avenue subway running under Park Avenue at that point, the fact that there is the Park Avenue tunnel used by autos, that forces the subway down to a lower level. And of course the fact that you need to deal with all the rest of the infrastructure like sewers, steam, water, and electric. Finally of course, just to make things more interesting (read you can't start dropping the MN tracks earlier to go under everything), is the fact that the LIRR is currently building the tunnels for the third (lower level) at GCT. I'm not sure that contruction as started on the station yet, but they have started boring the tunnels under Park Avenue for the East Side Access project.

Frankly with all the issues that would be associated with such a project, it would not surprise me if the short connection wouldn't cost more than the new tunnels under the Hudson which are far more straight forward.
 
And WAS to Hyannis might make a nice Acela route for service once every 3-4 hours if only there were electrification to Hyannis and enough Acela trainsets, even if the part north/east of Providence was on slower track.
My wife and I would jump on that Acela in Stamford in a heartbeat.

Putting WAS into the route makes a lot of sense.

It's also sad to think that, in an alternate universe with JFK and RFK alive most or all of these past decades, there would have been a lot more interest in a WAS to Hyannis route.
 
One other issue that would come up with an NYP (or WAS) to Hyannis train is that there are a finite number of slots over the Connecticut River bridge. Stealing a slot from Shore Line East or a Boston-bound train is probably not good for the overall system.
I see your point.

How feasible, then, is a spur from PVD to Hyannis?
 
While I'm not saying that it's impossible, connecting anything at GCT to NYP or the new NJT station isn't as simple as "let's dig a new tunnel. At GCT, there are loop tracks that run around all the stub end tracks. So you'd have to start by cutting those tracks, something that MN might not like.
Then you next have to deal with the fact that you've got the Lexington Avenue subway running under Park Avenue at that point, the fact that there is the Park Avenue tunnel used by autos, that forces the subway down to a lower level. And of course the fact that you need to deal with all the rest of the infrastructure like sewers, steam, water, and electric. Finally of course, just to make things more interesting (read you can't start dropping the MN tracks earlier to go under everything), is the fact that the LIRR is currently building the tunnels for the third (lower level) at GCT. I'm not sure that contruction as started on the station yet, but they have started boring the tunnels under Park Avenue for the East Side Access project.

Frankly with all the issues that would be associated with such a project, it would not surprise me if the short connection wouldn't cost more than the new tunnels under the Hudson which are far more straight forward.
Ok, but why does the Lexington Ave subway and Park Ave have to be involved at all? What's wrong with using the tunnel that already runs from GCT to Times Square?
 
One other issue that would come up with an NYP (or WAS) to Hyannis train is that there are a finite number of slots over the Connecticut River bridge. Stealing a slot from Shore Line East or a Boston-bound train is probably not good for the overall system.
I see your point.

How feasible, then, is a spur from PVD to Hyannis?
Tangentially, in the long run the Connecticut River bridge ought to be replaced with something higher that could be closed more often while still letting enough of the recreational boats through. But aside from people occasionally saying that here, I haven't seen anyone trying to do anything about making that happen. It might be good for someone to show up at a Connecticut Commuter Rail Council meeting and bring up this issue; regardless of whether a NYP to Hyannis train ever happens, Shore Line East would benefit from that sort of bridge improvement.

The issues I'm aware of with a PVD to Hyannis Amtrak train:

It would still go through the parts of Attleboro and Taunton where the neighbors don't want frequent trains. I don't know how much power those residents really have, and I don't know if a few trains a day to Hyannis would annoy them less than a few trains an hour that have been proposed for the commuter rail to Fall River / New Bedford which we know they oppose.

I'm pretty sure the tracks are all intact, assuming you wanted to go somewhere probably around 40-60 MPH and don't mind bothering the residents of Attleboro and Taunton.

There's a mix of Amtrak owned and operated track in Rhode Island, Massachusetts owned track that Amtrak has the contract to dispatch and maintain (so I don't know if Amtrak would need permission from Massachusetts to run more trains there or not), I suspect some of the track is owned by CSX, and then there's the Mass Coastal Railroad. Trackage rights need to be worked out along the whole route, in any case. I'm not sure either CSX or the Mass Coastal Railroad would have been in existance last time there was a passenger train there.

Amtrak has plenty of P42 locomotives, and they have some mothballed Amfleet I coaches. They could overhaul some Amfleet I coaches to be able to use them on this route.

Amtrak probably doesn't have any food service cars lying around, and doesn't have any easy way to order more that would be delivered quickly, so if this was going to run in the near future, it probably wouldn't have a food service car. Maybe a cart could be used to serve passengers at their seats.

The train would probably manage to lose money, which means that someone would have to subsidize it. Getting state and national legislative bodies to decide to spend money always seems to take time.

Amtrak would need to clean the train cars somewhere. Maybe the easiest thing to do would be to deadhead the trains up to the yards near South Station in Boston. Or if Amtrak became the railroad offering BOS to Hyannis service, they could possibly run each trainset under four train numbers in between cleanings: BOS to Hyannis, Hyannis to PVD, PVD to Hyannis, Hyannis to BOS. They might want to work out overnight parking at PVD and/or Hyannis, which may or may not introduce construction costs.
 
While I'm not saying that it's impossible, connecting anything at GCT to NYP or the new NJT station isn't as simple as "let's dig a new tunnel. At GCT, there are loop tracks that run around all the stub end tracks. So you'd have to start by cutting those tracks, something that MN might not like.
Then you next have to deal with the fact that you've got the Lexington Avenue subway running under Park Avenue at that point, the fact that there is the Park Avenue tunnel used by autos, that forces the subway down to a lower level. And of course the fact that you need to deal with all the rest of the infrastructure like sewers, steam, water, and electric. Finally of course, just to make things more interesting (read you can't start dropping the MN tracks earlier to go under everything), is the fact that the LIRR is currently building the tunnels for the third (lower level) at GCT. I'm not sure that contruction as started on the station yet, but they have started boring the tunnels under Park Avenue for the East Side Access project.

Frankly with all the issues that would be associated with such a project, it would not surprise me if the short connection wouldn't cost more than the new tunnels under the Hudson which are far more straight forward.
Ok, but why does the Lexington Ave subway and Park Ave have to be involved at all? What's wrong with using the tunnel that already runs from GCT to Times Square?

The fact that the Grand Central Shuttle runs in that tunnel pretty much stops you from using it. And this is a very heavily used route. Not to mention that once you get to TS, you have no place to go to bring the trains south to NYP. The shuttle tracks are orientated to run to the north, not the south. And there is no room to dig a new tunnel there, as you've got the #7, 1, 2, 3, A, C, E, N, Q, R, W trains all in that area. Then even if you could get past that problem, now you're entering Penn Station from the north, while all the tracks run east/west.

And back at GCT you'd have to run tracks right across the lower level of the station through the Oyster Bar, a landmark resturant, in order to link up with the subway tracks.
 
There is no way any railroad equipment will fit into any of the New York subway tunnels, and even if they could, they could not make a lot of the curves.

New York underground is an absolute maze of pipes and tunnels.
 
While I'm not saying that it's impossible, connecting anything at GCT to NYP or the new NJT station isn't as simple as "let's dig a new tunnel. At GCT, there are loop tracks that run around all the stub end tracks. So you'd have to start by cutting those tracks, something that MN might not like.
Then you next have to deal with the fact that you've got the Lexington Avenue subway running under Park Avenue at that point, the fact that there is the Park Avenue tunnel used by autos, that forces the subway down to a lower level. And of course the fact that you need to deal with all the rest of the infrastructure like sewers, steam, water, and electric. Finally of course, just to make things more interesting (read you can't start dropping the MN tracks earlier to go under everything), is the fact that the LIRR is currently building the tunnels for the third (lower level) at GCT. I'm not sure that contruction as started on the station yet, but they have started boring the tunnels under Park Avenue for the East Side Access project.

Frankly with all the issues that would be associated with such a project, it would not surprise me if the short connection wouldn't cost more than the new tunnels under the Hudson which are far more straight forward.
Ok, but why does the Lexington Ave subway and Park Ave have to be involved at all? What's wrong with using the tunnel that already runs from GCT to Times Square?

The fact that the Grand Central Shuttle runs in that tunnel pretty much stops you from using it. And this is a very heavily used route. Not to mention that once you get to TS, you have no place to go to bring the trains south to NYP. The shuttle tracks are orientated to run to the north, not the south. And there is no room to dig a new tunnel there, as you've got the #7, 1, 2, 3, A, C, E, N, Q, R, W trains all in that area. Then even if you could get past that problem, now you're entering Penn Station from the north, while all the tracks run east/west.

And back at GCT you'd have to run tracks right across the lower level of the station through the Oyster Bar, a landmark resturant, in order to link up with the subway tracks.
Ok, the taking out of the Oyster Bar is more than enough to convince me that that route isn't the way to go...
 
Subway cars have a much smaller loading gauge than Amtrak cars. They can go around sharper turns, negotiate smaller tunnels, and have the horsepower (due to their EMU nature) to up steep grades that would make most Amtrak equipment derail or beg for mercy.
 
A couple other thoughts about Hyannis service:

I was assuming a few posts above that Amtrak would run a PVD to Hyannis train. But maybe the Cape Cod Central Railroad could run it instead, in which case the rolling stock issues would become different. Or if Amtrak does run the train, maybe some of the Cape Cod Central Railroad's mainstenance infrastructure would offer an alternative to getting the train to the yard near South Station, though Amtrak may prefer to let their own crews do the work.

If there were an existing Amtrak-branded diesel PVD to Hyannis train, and if the tracks from PVD to NYP had infinite capacity for more trains, you still have the issue of needing to swap a locomotive somewhere unless the tracks all the way to Hyannis were electrified, and swapping an locomotive takes much longer than walking across the platform at PVD. On the other hand, I know AlanB has argued against walking across a platform in New Haven for the Vermonter in the cold of winter, but I tend to think of Hyannis as a summer destination; then again, I think it does indeed have some full-year residents.

Amtrak also basically does not have any extra electric locomotives, and while they could piggyback on an NJT order whenever one happens to happen, they probably don't want to collect more different models of catenary powered locomotive.

Yet another option would be to get an overhauled Budd RDC with HEP connectors and 125 MPH trucks, tow it from Washington to PVD on the back of an existing Washington to Boston Regional, and have the main train drop the RDC off in Providence, at which point it would start up its diesels and go to Hyannis. But that would probably create a 10 minute delay in PVD for the Bostonians while the brake test is done on the slightly shortened train that goes to Boston.
 
Ok, but why does the Lexington Ave subway and Park Ave have to be involved at all? What's wrong with using the tunnel that already runs from GCT to Times Square?
In addition to all the points the others have brought up, there is also the matter that the FRA has a certain amount of concern for passenger safety in collisions. There are a lot of rules that a passenger railroad has to follow that subway systems are exempt from. For a subway system to remain exempt from the railroad regulations, there are some very, very limited circumstances in which subway track can be connected to the national rail system; I believe the rule is something along the lines that you can have a siding that's one or two cars long which has a Y arrangement that connects it to both the national rail system and the subway system. The point of this is largely to make sure that you never have a heavy freight train collide with a subway train (except possibly when the subway cars are being delivered from the manufacturer, but at that point the subway cars probably don't have passengers in them). Europe probably doesn't have such strict rules about this, but they solve this particular problem (to one extent or another) by not running such heavy freight trains.
 
While I'm not saying that it's impossible, connecting anything at GCT to NYP or the new NJT station isn't as simple as "let's dig a new tunnel. At GCT, there are loop tracks that run around all the stub end tracks. So you'd have to start by cutting those tracks, something that MN might not like.
Then you next have to deal with the fact that you've got the Lexington Avenue subway running under Park Avenue at that point, the fact that there is the Park Avenue tunnel used by autos, that forces the subway down to a lower level. And of course the fact that you need to deal with all the rest of the infrastructure like sewers, steam, water, and electric. Finally of course, just to make things more interesting (read you can't start dropping the MN tracks earlier to go under everything), is the fact that the LIRR is currently building the tunnels for the third (lower level) at GCT. I'm not sure that contruction as started on the station yet, but they have started boring the tunnels under Park Avenue for the East Side Access project.

Frankly with all the issues that would be associated with such a project, it would not surprise me if the short connection wouldn't cost more than the new tunnels under the Hudson which are far more straight forward.
Maybe part of the answer is to connect only the lower level(s), then. WAS is an example of a station with a terminal that goes in only one direction on the upper level, and a lower level with through tracks. There's a proposal to have BOS and BON end up being similar to WAS in this regard. At least one if not both of the commuter terminals in the center of Philadelphia were abandoned when their tunnel connecting the stations was built. (I personally think the surface platforms at BON should be abandoned once the NSRL is built and electrification happens everywhere, but the authors of the NSRL study don't agree with me.)

Is there anything that would prevent building a tunnel by which the MTA's tracks to upstate New York and to Connecticut could reach the MTA's under construction third, lowest level at GCT?

I'm also not sure how much cutting the loops is really a problem. They might not be needed for through trains to NYP. Though if the MTA were running significantly more trains than NJT, some trains certainly would have to continue to turn around at GCT and or NYP. (And I'm also making the perhaps overly optimistic assumption that NJT and the MTA could combine their efforts and through run many/all of their trains across their systems.)

Do the subway and utility lines get in the way for the level that's currently the lower level at GCT, and that will become the middle level after the East Side Access project is done, or is this only a problem for the upper level?

How many tracks would be where if this were all done? I believe there are going to be four tracks heading to New Jersey total once THE Tunnel is constructed, and a GCT-NYT connection would possibly make the existing Empire Connection obsolete, so four tracks from NYP to GCT might make sense. Is there a level of the existing Penn Station that's low enough that it could reasonably get underneath everything to get to some level of GCT?

Would it be possible to construct things so that an LIRR train could come across the river from Long Island, stop at GCT, continue to NYP, and then head back across the river back to Long Island?
 
While I wish I could catch an Amtrak train from the granduer of Grand Central Terminal, I fail to see much in the way of an advantage to such a link up.
 
If there were an existing Amtrak-branded diesel PVD to Hyannis train, and if the tracks from PVD to NYP had infinite capacity for more trains, you still have the issue of needing to swap a locomotive somewhere unless the tracks all the way to Hyannis were electrified, and swapping an locomotive takes much longer than walking across the platform at PVD. On the other hand, I know AlanB has argued against walking across a platform in New Haven for the Vermonter in the cold of winter, but I tend to think of Hyannis as a summer destination; then again, I think it does indeed have some full-year residents.
Summer service would be the only way a PVD to Hyannis train could be profitable - conceivably it could support some kind of reduced service all year.

Question (with apologies for my ignorance): why can't a slower deisel train run between PVD and Hyannis - a train that passengers on WAS or NYP to BOS could catch in PVD? Where does the need for swapping come in?
 
Amtrak also basically does not have any extra electric locomotives, and while they could piggyback on an NJT order whenever one happens to happen, they probably don't want to collect more different models of catenary powered locomotive.
Well if NJT were to go ahead with obtaining a dual mode locomotive, then Amtrak could piggyback on that order.
 
Maybe part of the answer is to connect only the lower level(s), then. WAS is an example of a station with a terminal that goes in only one direction on the upper level, and a lower level with through tracks. There's a proposal to have BOS and BON end up being similar to WAS in this regard. At least one if not both of the commuter terminals in the center of Philadelphia were abandoned when their tunnel connecting the stations was built. (I personally think the surface platforms at BON should be abandoned once the NSRL is built and electrification happens everywhere, but the authors of the NSRL study don't agree with me.)
Only the old Reading terminal was abandoned when the Center City connection was built. On the Pennsy side they only essentially knocked 4 holes in the wall to connect with the new tunnel to the new Market East station

Is there anything that would prevent building a tunnel by which the MTA's tracks to upstate New York and to Connecticut could reach the MTA's under construction third, lowest level at GCT?
Yes, Metro North uses under-running third rails, while the LIRR uses over-running third rails.

I'm also not sure how much cutting the loops is really a problem. They might not be needed for through trains to NYP. Though if the MTA were running significantly more trains than NJT, some trains certainly would have to continue to turn around at GCT and or NYP. (And I'm also making the perhaps overly optimistic assumption that NJT and the MTA could combine their efforts and through run many/all of their trains across their systems.)
I'm not sure that it would be a huge problem, but AFAIK MN does still use the loop tracks. Most trains do turn right on the platform, but not all.

Do the subway and utility lines get in the way for the level that's currently the lower level at GCT, and that will become the middle level after the East Side Access project is done, or is this only a problem for the upper level?
It's a problem for both levels. You've got the Lexington Ave line that transistions from Lex to Park at one level, the Shuttle at yet another level, and the #7 at the lowest level. So you're basically fighting subway tracks on three levels. It's probably still possible to push something through, but it won't be easy.

How many tracks would be where if this were all done? I believe there are going to be four tracks heading to New Jersey total once THE Tunnel is constructed, and a GCT-NYT connection would possibly make the existing Empire Connection obsolete, so four tracks from NYP to GCT might make sense. Is there a level of the existing Penn Station that's low enough that it could reasonably get underneath everything to get to some level of GCT?
I don't see why more than 2 would be needed, but in theory you could certainly run 4.

Would it be possible to construct things so that an LIRR train could come across the river from Long Island, stop at GCT, continue to NYP, and then head back across the river back to Long Island?
Well anything is possible, just not sure that it's needed or practical. But it wouldn't be that hard to do, once a track was built, since you'd then run through GCT and then just reverse in NYP or the East Side yard.
 
Amtrak also basically does not have any extra electric locomotives, and while they could piggyback on an NJT order whenever one happens to happen, they probably don't want to collect more different models of catenary powered locomotive.
I think Amtrak would love to get their hands on ALP-46a locos. But I think the rules under which Amtrak bids for things rules out the Daimler-Benz designed, largely German-built Class 101-based locomotive.
 
Question (with apologies for my ignorance): why can't a slower deisel train run between PVD and Hyannis - a train that passengers on WAS or NYP to BOS could catch in PVD? Where does the need for swapping come in?
I probably wasn't being clear.

If you wanted to have passengers board a particular Amfleet I coach in NYP and stay in that coach until they get to Hyannis, and if there's no electrification from PVD to Hyannis, the train has to be powered by an electric locomotive part of the way (because diesels are not allowed to run inside the New York City tunnels) and a diesel locomotive in the areas where there is no electrification. While there are circumstances where dual mode locomotives can be usable, and while it would be possible to simply put one locomotive of each type on the train and haul a locomotive that wasn't running, a more likely approach to dealing with this would be to replace the locomotive at some point during the trip.

The Regional trains that run to Newport News do this type of locomotive swap, usually at WAS; there's no electrification south of WAS. There are also a few Springfield trains that do this type of swap in New Haven, and before the electrification north of New Haven was completed, all BOS to NYP trains swapped locomotives at New Haven. The Lake Shore Limited swaps between a dual mode locomotive (diesel and third rail) and a pair of plain diesel locomotives at ALB.

Of course, if the passengers get out of the train at PVD and walk across the platform, they can walk over to a train that has a different type of locomotive than the train they were just on, and the brake test can be performed before the passengers start boarding.
 
Question (with apologies for my ignorance): why can't a slower deisel train run between PVD and Hyannis - a train that passengers on WAS or NYP to BOS could catch in PVD? Where does the need for swapping come in?
I probably wasn't being clear.

If you wanted to have passengers board a particular Amfleet I coach in NYP and stay in that coach until they get to Hyannis, and if there's no electrification from PVD to Hyannis, the train has to be powered by an electric locomotive part of the way (because diesels are not allowed to run inside the New York City tunnels) and a diesel locomotive in the areas where there is no electrification. While there are circumstances where dual mode locomotives can be usable, and while it would be possible to simply put one locomotive of each type on the train and haul a locomotive that wasn't running, a more likely approach to dealing with this would be to replace the locomotive at some point during the trip.

The Regional trains that run to Newport News do this type of locomotive swap, usually at WAS; there's no electrification south of WAS. There are also a few Springfield trains that do this type of swap in New Haven, and before the electrification north of New Haven was completed, all BOS to NYP trains swapped locomotives at New Haven. The Lake Shore Limited swaps between a dual mode locomotive (diesel and third rail) and a pair of plain diesel locomotives at ALB.

Of course, if the passengers get out of the train at PVD and walk across the platform, they can walk over to a train that has a different type of locomotive than the train they were just on, and the brake test can be performed before the passengers start boarding.
Thanks. They used to do a swap at NHV, until all the tracks to BOS were electrified.

It seems like walking across the platform at PVD would be the way to go, as far as simplicity. And since summer would by far be the peak time, freezing cold weather shouldn't be a problem.
 
Do the subway and utility lines get in the way for the level that's currently the lower level at GCT, and that will become the middle level after the East Side Access project is done, or is this only a problem for the upper level?
It's a problem for both levels. You've got the Lexington Ave line that transistions from Lex to Park at one level, the Shuttle at yet another level, and the #7 at the lowest level. So you're basically fighting subway tracks on three levels. It's probably still possible to push something through, but it won't be easy.
I wonder if this argues for building the lowest level lower than they'd been planning to build it.

How many tracks would be where if this were all done? I believe there are going to be four tracks heading to New Jersey total once THE Tunnel is constructed, and a GCT-NYT connection would possibly make the existing Empire Connection obsolete, so four tracks from NYP to GCT might make sense. Is there a level of the existing Penn Station that's low enough that it could reasonably get underneath everything to get to some level of GCT?
I don't see why more than 2 would be needed, but in theory you could certainly run 4.
The Boston NSRL proposal contemplates both two track and four track versions. The four track version increases the number of trains that take passengers to both North Station and South Station (and Central Station, if it gets built) without passengers having to change trains.

Given how huge New York City is compared to Boston, it seems unlikely to me that having fewer tracks for a seemingly-equivalent thing in New York City would make sense. Then again, I think GCT is closer to NYP than BON to Aquarium or Aquarium to BOS. (Central Station is expected to be near the existing Aquarium station.)

Given that NYP is going to have 4 leads to New Jersey and four to Long Island, and GCT is going to have 4 leads to Metro-North territory and two to Long Island (I think), if through running is something people believe is valuable, it might make some sense to have four through tracks from New Jersey to Metro North territory, and to try to get those trains to completely stop turning around in Manhattan at all, and configure the tracks so that trains that arrived in Manhattan via ESA would stop at GCT, then NYP, then continue back to Long Island via the southern four tracks, and trains headed to the ESA tunnels would reverse that procedure. But then there would still be two LIRR lead tracks at NYP for which the trains would need to turn around in NYP.

Large amounts of catenary installation might get rid of the third rail compatibility issues.
 
Do the subway and utility lines get in the way for the level that's currently the lower level at GCT, and that will become the middle level after the East Side Access project is done, or is this only a problem for the upper level?
It's a problem for both levels. You've got the Lexington Ave line that transistions from Lex to Park at one level, the Shuttle at yet another level, and the #7 at the lowest level. So you're basically fighting subway tracks on three levels. It's probably still possible to push something through, but it won't be easy.
I wonder if this argues for building the lowest level lower than they'd been planning to build it.
That wouldn't help, since the point of any connection between GCT and NYP is to interline NJT and MN. Making the new LIRR level lower does nothing to solve the above problem and the LIRR doesn't need to run between GCT and NYP. There is no point for them to do so. They'll just switch have pax continue to switch trains in Jamaica like they do now, to pick the correct train to either GCT or NYP.

How many tracks would be where if this were all done? I believe there are going to be four tracks heading to New Jersey total once THE Tunnel is constructed, and a GCT-NYT connection would possibly make the existing Empire Connection obsolete, so four tracks from NYP to GCT might make sense. Is there a level of the existing Penn Station that's low enough that it could reasonably get underneath everything to get to some level of GCT?
I don't see why more than 2 would be needed, but in theory you could certainly run 4.
The Boston NSRL proposal contemplates both two track and four track versions. The four track version increases the number of trains that take passengers to both North Station and South Station (and Central Station, if it gets built) without passengers having to change trains.

Given how huge New York City is compared to Boston, it seems unlikely to me that having fewer tracks for a seemingly-equivalent thing in New York City would make sense. Then again, I think GCT is closer to NYP than BON to Aquarium or Aquarium to BOS. (Central Station is expected to be near the existing Aquarium station.)

Given that NYP is going to have 4 leads to New Jersey and four to Long Island, and GCT is going to have 4 leads to Metro-North territory and two to Long Island (I think), if through running is something people believe is valuable, it might make some sense to have four through tracks from New Jersey to Metro North territory, and to try to get those trains to completely stop turning around in Manhattan at all, and configure the tracks so that trains that arrived in Manhattan via ESA would stop at GCT, then NYP, then continue back to Long Island via the southern four tracks, and trains headed to the ESA tunnels would reverse that procedure. But then there would still be two LIRR lead tracks at NYP for which the trains would need to turn around in NYP.

Large amounts of catenary installation might get rid of the third rail compatibility issues.
Yes, there will be 4 tunnels to NJ once "The Tunnel" is completed. However, two tunnels will only serve the existing NYP and the two new tunnels will only serve the new 34th Street station that will be built under 34th Street. So that comlicates things considerably. And as I pointed out above, the LIRR will not be using any connection between GCT and NYP. They don't need it.

Not to mention that a connection that would allow the LIRR to run from GCT to NYP and then return to Queens without turning the train would not only increase the costs of the project, it would render the connection useless to MN and NJT as the LIRR would need the tunnel to enter NYP from the western side, while NJT & MN would need the tunnel to enter NYP from the eastern side.
 
Not to mention that a connection that would allow the LIRR to run from GCT to NYP and then return to Queens without turning the train would not only increase the costs of the project, it would render the connection useless to MN and NJT as the LIRR would need the tunnel to enter NYP from the western side, while NJT & MN would need the tunnel to enter NYP from the eastern side.
Also not mentioning that the Long Island and Metro North electrification systems are beyond incompatible, they are mutually exclusive.
 
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