What you are describing, in my opinion and experience, is not typical for a child with properly functioning digestive system.
My child has food intolerances and allergies. The allergist and most doctors don't 'believe in' food intolerances because it can't be measured. We had a food intolerance turn into an actual food allergy.
I CAN measure when my child is not feeling well, and that is the bottom line.
The pain, the eating only certain foods, the stool issues - all scream food intolerance to me. Do some research online about it, and you'll see what I mean. A food journal should help you figure out which foods to avoid.
For my child, all the carb heavy stuff you have listed (waffles, french toast, nuggets(the breading)) would indicate gluten intolerance.
All the yogurt, ice cream would be dairy intolerance.
For my son berries were phenol intolerance.
You'll have to learn which components make up different foods.
Here's an interesting point - the foods that are most problematic are the ones they most crave!
Gluten, casein, soy, and phenols are often things kids have problems with. Some others are egg, corn, nuts. Thus the huge increase you see in gluten-free and allergen free and organic foods on the market today. There are great books available at amazon.com to help you decipher your child's food issues.