The body was made for whole, real foods, and whole, real foods for the body. (Paraphrase from one of the Pauline epistles. When that was written, processed junk had not been invented.) However, if you have been eating little to no real foods (i.e., you considered French fries a veggie and not the little sticks of artificial grease they really are), for years or your entire life, your body is learning to adjust. Also, the diarrhea might just be from not enough water, not enough fiber, I'm not really sure. The last time I had it was just from a bug.
When I wake up with a funky feeling tummy, it's usually because I didn't have my bedtime snack and I'm really hungry.