Just a warning about Amtrak...I've used it twice, once across the country and once up the west coast from LA to Seattle. Both experiences were disasters. Filthy conditions, WAY late on arrival, unfriendly and uninformed staff. Etc. I'll never use them again. It sounds like others have had much better experiences, so maybe I just hit the wrong train two out of two times.
A few years back, I did the Willamette Valley from one end to the other, and I needed to get to Portland from Eugene. Amtrak has a train going through there with roll on/off service, but availability and schedules did not work out for me. Amtrak also has a bus line going through there, with a bike option. I got one cargo bay to transport my bike and gear. The staff on both ends were wonderful. I was personally met in Portland by the station master, who made sure I had a safe route out of Portland.