My Drs kept telling me it was nothing to do with what I was eating because all the conventional tests are coming back negative. So if all your conventional tests come back negative that is good as there isnt anything seriously wrong that they can find. But it is frustrating at the same time for sure. Be proactice in your son's health and even if your Drs say stool tests are bogus and outdated request one to be sure or check out Enterolab.
Even if your celiac tests come back negative it doesnt mean he doesnt have an intolerance to gluten (as was the case with me). Cut out dairy and gluten for a week and see if that helps. Go with a bland diet of rice, grilled chicken or white fish(no marinades) and well cooked green beans for dinners. For breakfast try some hard boiled eggs, and turkey bacon (no pork). Bananas are good, as is apple sauce. No sodas or juices. Try some pedialyte if you feel he is getting dehydrated. You can also try some gluten free pasta but a lot of that has corn in it, and there might be an intolerance to corn, soy, wheat, dairy, nuts etc.
I had tests done through Enterolab which tests your stools for antibodies produces by gluten, dairy, soy, corn, nuts, etc. Might be worth looking into IMO.