Just a couple of things:

Your shorts should be picked to fit your butt. If the belly being squished is a real issue, take a look at bib shorts.

For training purposes, there are lots of programs both online and in books. Take a look at some century training programs for example. Riding the trainer is boring, especially if you are just pedaling. There are DVDs, Spinervals and Carmicheal Training for example, to use with the trainer. Also if you have anything you used with running, like mp3s with intervals, they work with the bike.

Ditto what was said about possibly needing a different saddle as well as you may need to be properly fit on your bike.

Also agree with the suggestion that a road bike of some kind will make a ride like RAGBRAI much easier. That come in models for all types of terrains. Mine's pure road and I've ridden it on some pretty rough terrain.

BTW, congrats on doing RAGBRAI. Did you see Lance?