Have you talked to a dr about potential food allergies? Dairy and gluten are already ruled out but what about soy, food dyes, msg, nuts? Also, although it seems very doubtful because of his age, is it possible he has heartburn?
I would definitely take him into the pediatrician as soon as possible (preferable three weeks ago). You may not be looking at food allergies but something more serious. The Dr. could order a Barium study or even even Ultrasound to see if there is any problem with blood flow to the GI tract. You said he had regular bowel movements... but are they a little explosive? All the same, If he were my baby, I would have him checked out. It may be nothing but, it could be a sign of problems. Good luck
Possibly even parasites (raw diet)
Thanks everyone for your ideas, we have been working with doctors for the last two years and not getting very far. To clarify: by a raw diet, I meant most of his food is natural like our great grandparents would have eaten, sorry for the confusion.