I didn't have any issues with the elevation. You can feel your ears pop a bit, but you just yawn or swallow like you would when flying. When we stopped in Grand Junction and Denver, I noticed myself getting short of breath a little sooner than usual, but it wasn't anything terrible. I just had to remember not to walk so fast.
I'm claustrophobic, and I feel perfectly comfortable in a roomette. The windows are large, so it doesn't feel like there's a wall next to you. If you leave the door and curtain open, it's even better. (You also get more air circulation.) If you want privacy but still want fresh air, you can just close the curtain. It has a long strip of velcro to help keep it closed, and it covers most of the doorway.
I cannot handle the upper bunk, as it is too close to the ceiling for my comfort. Some people have nicknamed it "the coffin". If your wife is not claustrophobic, I would ask her to sleep up there while you take the bottom bunk. If you feel a little closed-in with the door shut at night, you can open the curtains and look out the window. I love looking out the window while laying in bed.
Sometimes the cafe attendant has packs of Amtrak cards to sell, but those are the only souvenirs I've seen. I was able to buy some things at the shop in Grand Junction. They also sell ice cream; I don't think a single person walked out of there without an ice cream treat.
