Scott from Indianapolis on 8/21/2013 9:54:40 PM:
I actually did a very similar trip in July, except we did it in reverse...we started in Jeff City, rode to Boonville the first day, then rode to Sedalia the second day and caught Amtrak back to Jeff City.
Nonetheless, both Amtrak stations are easy to bike to (just map them out ahead of time) but the Amtrak station in Jeff City is located by the state capital building. It's probably about a 3 1/2 mile ride from the main Jeff City trailhead (North Jefferson) and includes crossing the river on the bridge to get into Jeff City. There's a spur trail that takes you from the Katy Trail to the bridge and the bridge to Jeff City has a dedicated bike and pedestrian lane which is completely separated from traffic by a barrier, very safe. You then have to ride on the city streets to the capital but there was very little traffic.
I had no trouble making bike reservations using the Amtrak website. I think it's 10 bucks per bike or something like that. We were the only ones boarding with our bikes. We boarded onto the cafe car. We had to carry our bikes onto the train and then we strapped them to the new bike racks which were set up in the cafe car. The Amtrak guys even offered straps to secure the bikes to the rack.
I hope that helps you plan your trip.