Congrats on doing RAGBRAI! With a hybrid that's quite an accomplishment.

Agree with the others on looking at a cross bike, it would probably be able to handle unpaved trails pretty well.

As for training, I've never done RAGRBAI, but I've done Bike Across Kansas. The more miles before you go, the better. However, some periodization with high mile weeks and low mile weeks, as well as interval training can help. I followed the endurance plans in this book:

The Female Cyclist

Or one of the century training plans that you can find online could also help.

Some of your other problems would probably be helped by a good bike fit, as well as some experimenting with different saddles and shorts.

Good luck.