There are several reasons why I don't do any bike touring, and food is one of the big ones. I've found that any stomach problems I might have during long rides are caused by eating the wrong foods the day or so before the ride. It's easy enough to control that when I'm riding a couple of times a week during my normal routine, but I worry about having to rely on eating out all the time on multi-day tours. Just going out of town for a one-day bike ride can be a challenge.

Do you keep a food diary? That might help to show patterns that you can correlate with how you feel, especially if you include notes on your activities each day.