It looks like you have received some good advise. My son has digestive issues and was born with a digestive disease. I also suffer from a very sensitive digestive system.
It is good to have all the tests to rule out the more serious digestive disorders. When they do the colonoscopy they can also to a biopsy. This is how we learned my son was allergic to dairy protein.
I'm going to talk to my doctor about celiac, they can test for this through a blood test, thought I hear it can be inconclusive.
You can also try an elimination diet and then begin adding back in one food group at a time. You just keep a journal of food and mood/bms and such to see how he reacts. Talk to your dr. I make this sounds easy, but it can take some work.
Also, one person wrote in about raw veggies, and nuts. These contain fiber, but can be very difficult to digest. Also, nuts can be culprits of allergies and are very tough on digestive systems especially with certain disorders. I would suggest not giving these foods to your son for now. Bananas and applesauce (go organic and no to low sugar) are easy to digest fruits and steamed or cooked veggies are also more easily digested than raw.
I hope this helps and I hope your son's issues turn out to be a simple allergy.
T.