AlanB I read your entire trip report. Very well done. You used some terminology and acronyms that are obviously understood by experienced railfans but not me.
Please don't hesitate to ask me questions, either publicly or privately via Private Message, if you want to know.
Nevertheless, I got a good feel for the potential problems and delays that may be encountered. Now I realize that the 5.5 hours between 29's scheduled arrival at CUS and 7's (EB) departure could be trimmed down by delays between Washington DC and Chicago. And I will inform my party that we should not count on arriving at Seattle at the scheduled time. Lots of potential for delays along that 2 1/2 day trip. The NEC has kept almost impeccable schedules from our experience, but they don't share the tracks with freight trains (at least I've never seen one).
Yes, the odds are very good that you will make the connection, but they are also pretty good that you will be at least a little late.
Freight can be found on the NEC, but then it mostly only runs at night. Even then it is still at the mercy of the Amtrak dispatchers.
By the way I should have also mentioned that you guys get to take advantage of the Club Acela lounge in DC (well they do, you can't since you're in coach) and the Metropolitan lounge in Chicago. These lounges are a nice quiet refuge in the often-bustling train station. They have nice plush chairs, conference rooms, computer terminals, newspapers, TV's, free soft drinks, juices, coffee, tea and clean safe bathrooms. They also allow you to board your train before the rest of the masses.
In DC the Club Acela Lounge is located behind the information kiosk, which is in the center of the waiting areas between gates D & E. There are two large wooden doors there, ring the bell to the right of the door and the attendant will let you in. Show your tickets and you’re in. They will escort you to your train when it’s time.
In Chicago the lounge is called the "Metropolitan Lounge". It is located on the lower level of Union Station, which is also the track level. If you are standing in front of the Amtrak ticket windows, then the Amtrak waiting area is to your left. When you enter the main Amtrak waiting area through a sliding glass door, just walk forward and slightly to the left. There should be another sliding glass door along with a sign, unless they've changed the entrance in the last few months. Again, just show your tickets and relax.
They'll also give you a card that contains the time that you need to return to the lounge by, in order to board the train and not miss it. If you do leave the lounge, take this card with you as it is also your pass for reentering the lounge. Just wave it at the attendants as you walk in and one will usually look up and acknowledge you and the card. Note the Chicago lounge can be very busy and it sometimes can be hard to get a seat, but you still get the free stuff and priority boarding.
Note: They will make you leave your carry-on bags in the luggage room inside the lounge, you cannot take them to your seat due to the crowded nature of the lounge. There is a redcap manning this room who will give you a claim check for your bags, such that you can claim them shortly before you board the train. One nice advantage of this is the fact that you can park your carryon bags here, while you wander around Chicago and do lunch, assuming that your trains arrive on time.