I've had good luck using Amtrak to get places. I've never tried to use them to plan my vacation from the ground up. That may be outside of their training. Starting with a destination seems like reasonable request.

You have a lot more routes than I do here, so you also have a lot more options. In my area I haven't found that there is a lack of baggage stations, just that there are more stations that don't handle baggage. If you start out with nothing more than a direction or train line, you can download the schedule for that line and see all the stations that have baggage service.

I've gone in-state a number of times because there are some in-state lines that don't require bike boxing. Just reserve a spot and you're set. Earlier this month I took my first long-distance trip. I knew I was going to be in north east Ohio, and looking at a couple of routes, it seemed clear that Cleveland was my closest station option that took baggage. I had to swich trains in DC, and the connection was kind of tight given that some trains can run late. The ticketing system wanted me to stay in DC overnight rather than count on making my connection, but I decided to risk it, and just bought my tickets on two transactions. Got to the Cleveland station a couple of hours ahead of time since it was my first time traveling with a boxed bike. Bought a box. My bike fit in easily, although I had to remove my handlebars(and pedals, which is standard), which I expected. Had lots of time sort out the rest of my baggage. Checked my bike and carried everything else on. No problems. Amtrak folks were helpful and pleasant. Got into DC on time, claimed my bike, rechecked it on the next leg, and finished my trip. Again everyone was pleasant and helpful, even though I confused them by having booked the two legs of my trip separately. I had to pay a 2nd checked bike fee as a result, although I got the impression that I could have gotten out of that if I had complained, but I didn't want to make a fuss. Especially since the confusion was a result of my tricking the ticketing system into letting me make a tight connection. Next train left on time. Got home on time. The bike was reassembled in minutes. I persuaded my wife to pick up the rest of my luggage, so that I didn't have to repack the bike. So I was able to make great time home from the station.

Before the trip, I thought the worst part of my vacation was going to be having to travel with my bike, but Amtrak made that really easy, and now I'm looking for other places I can go.