I'm not sure where you're coming from, so I don't really know what to suggest as far as the trains are concerned. Due to their schedule and the lack of a decent connection between Grand Rapids and Lansing and Grand Rapids and Kalamazoo, it's kind of hard to combine all three.
If you want to do anything in Michigan, you're going to need a car. Our cities do not have the transit like you would find in large cities like Chicago. Yes, we have some local buses, but they're basically useless for sightseeing. Plan to rent a car when you visit each major city.
You could take the Pere Marquette from Chicago to Holland and spend some time there. I also suggest completing the trip to Grand Rapids. GR is the largest city in western Michigan and has a plethora of museums and restaurants. I suggest the Frederick Meijer Gardens & Sculpture Park, which is open year-round.
From GR, take 131 south to Kalamazoo. Park downtown and enjoy the pedestrian mall with all of its boutique shops. If you like beer, you're in luck. The entire east end of downtown has developed into umpteen craft breweries, some with incredible food. Arcadia is my favorite; if you sit near the rear of the building, you'll have a view of the river, and you can watch Amtrak go by.
After you eat, drive west on Kalamazoo Ave until you get to the Stuart neighborhood (just a mile or so). Enjoy the gorgeous historic homes and then continue west. You'll go through a tight S-curve and up a hill (West Main Hill), where you'll happen upon
Henderson Castle. Spend the night there. Go to the rooftop and enjoy a view of Kalamazoo and the valley while relaxing in the hot tub.
From Kalamazoo, you can take the Blue Water to Lansing and Port Huron or the Wolverine to Ann Arbor and metro Detroit. There is no way to go to Port Huron and back; it requires an overnight. You could, however, take it as far as Lansing and then come back. Lansing is our capital, so you could check out the Capitol Building and the Michigan History Center.
I used to live in Ann Arbor. Here are my favorite things:
- Take a stroll along Main St. and Liberty St. Great restaurants and shops. True, quirky Ann Arbor culture. Look for the
fairy doors.
- Go book shopping at
Literati (new books) and
Dawn Treader (used books). If you're on the west side of town, you absolutely have to go to
Nicola's Books.
- Walk through the "Arb" (
https://mbgna.umich.edu). There's a great path along the river.
- Go to the Law Quad at U of M. You'll feel like you're walking around Oxford or Hogwarts.
- If you're over by Michigan Stadium, which you should be if your wife is a big Michigan fan, stop and get ice cream at
Washtenaw Dairy.
- If you want to eat somewhere rail-related, go to either the Gandy Dancer ($$$$) or Sidetrack's (in Ypsilanti, just a few miles away). Sidetrack's is more affordable and has incredible food. I used to eat there all the time. Amtrak passes right in front of the restaurant; when you're seated on the patio, it's tradition to raise your glass and "toast" the train passengers. It has a neighborhood pub feel. Gandy Dancer is much fancier and is usually reserved for special evenings. On the other hand, it's housed in the historic train depot and sits right on the tracks (next to the "new" Ann Arbor station), so it's nice if you want some history and a romantic meal.
- Zingerman's Deli in Kerrytown. You'll thank me for this one.
So, onward to Detroit. I second (third?) everyone's recommendation to visit the Henry Ford Museum and Greenfield Village. While the museum is practically on top of the Dearborn Amtrak station, it's actually a mile walk from the station to the entrance to the museum, as you have to go around the block. I really wish they'd create some kind of pedestrian bridge, as they could attract a ton of visitors that way.
Anyway, once you get into Detroit proper, go to Lafayette for a coney dog. They have a rivalry with their next-door neighbor, American, for who has the best coney, so if you want to get in on that, go to both. They're owned by the same family, so it's a friendly rivalry.
I say Lafayette's coneys are better, and I like their restaurant better - very old school Detroit, with the turquoise/black tiles and everything. American is more modern diner.
Once you do that, check out everything Detroit has to offer. Take a ride on the People Mover. Check out the old theaters. Admire the gorgeous architecture. Many of the buildings have been purchased and restored (yay!) or are in the process of being restored (double yay!). You can also go to a few casinos, and if you have your passport, you can take a cab across to Windsor to check out Canada for a bit.
I don't know if you like books, but you're getting another suggestion:
John King Used & Rare Books. I can't even call it a bookstore. The building is an old leather glove factory, and it's four or five stories of thousands and thousands of books. It hasn't been renovated, so it still has that industrial look and feel - old wooden floors, piping, naked bulbs for lights, etc. It really is a gem.
Check out the Riverwalk and the RenCen (Renaissance Center). While there, head to nearby Greektown to see the old churches and restaurants. I love the Greektown streets at night, with the string lights and flags. It always feels like a festival.
Do not be scared of Detroit. If you're downtown during the day, you're going to run into a ton of other people who are going to shows, sporting events, the casinos, restaurants, etc. Greektown is extremely popular, but not crowded. If you feel like you're heading into an area with fewer people and things feel "off", just turn around.
Speaking of "off", the area around Michigan Central Station is kind of sketchy. I definitely recommend heading over to check out the building, but I wouldn't recommend parking and walking around. I don't say that to scare you - I've been there
plenty of times by myself - it's just so close to downtown that it can feel like it's ok to let your guard down a bit.
If you have any questions, please let me know. Michigan is a HUGE state, so I'm always at a loss when people ask for suggestions. Those are the highlights, but if you provide a little more info about your interests, I'm sure we can help you create a nice itinerary.