We've traveled from MN to IN several times since our daughter was born over 2 years ago. We've driven the car (BAD IDEA), taken the train and have flown. Flying has the advantage of getting there quickly, but the stress of it all is a lot and still takes a fair amount of time when you figure in 2-3 hours to park the car, get tickets, go through security, wait at the gate and then the actual plane ride and then waiting to get off the plane, walk through the airport, wait for checked baggage, get a rental car, etc.
The disadvantage to the train is that it takes as long as driving (maybe longer) and you are "stuck" on the train until your destination. The advantages, however with a baby, are great. You do not need to stay in your roomette (we never had one). You can walk about the most of the train the entire time, there is usually an observation car that has tables and "captains" chairs for you to sit in and look at the beautiful scenery. You get to see a lot of countryside that is only visible by train (if you travel during the day!) If you were to sit in the coach cars for a while, the seats recline with foot rests and there are electrical outlets at each set of seats. There is plenty of floor space through-out the lower levels of the cars to put out a blanket for baby to play. You can bring your own food and drink so you can keep your money in your wallet. The snack bar (in the observation car) and the dining car are very expensive.
Pack for baby: Your stroller that holds your infant seat, infant seat, a boppy (for breastfeeding), a bag of toys, blankets (ones that can go on the ground and put away to be washed later), and a sling if you use one. I like your idea to have baby sleep in the car seat at night. It sounds the safest.
Also bring an easy to use cooler for your food and drinks. Try to under-pack than over-pack. Most of your luggage will be stored by Amtrak personnel under one of the cars (similar to checked baggage at airports). You CAN take your stroller, car seat, cooler, and smaller bags on board with you. The Amtrak employees were very helpful with helping us get our things on. There is a luggage area on the bottom level of most of the coach cars. That is where we put the stroller and one of our larger suitcases (we missed the very strict rule of needing to check our bags by the 30 minutes prior to departure).
Hope this helps. We plan to use the train to go back to IN once baby #2 arrives. It is much less stressful than flying and breastfeeding and baby's napping are barely interrupted. :)