Is he too small for a pill cam? Has anyone considered a balloon endoscopy?
Has he done a fecal calprotectin test? If this comes back negative for bowel inflammation then I would proceed to do elimination diets, starting with gluten. Even if he has not been found to have celiac disease, he can still have a gluten intolerance.
Inflammatory markers in blood tests are of some concern. Has he been seen by rheumatology?