That's a tough spot and I sympathize!
I have problems with grains -- wheat in particular -- but I don't think it is necessarily an allergy. The distinction can be subtle, but important. I can tell that I'm one of those people for whom wheat lectins bind well to active sites in the cells of my stomach lining. Too much wheat means that the regeneration of my stomach lining is impaired and I develop severe acid reflux. This isn't an allergy as there is no immune response happening.
The reason I'm going into this is that foods can be incompatible with a person (such as wheat's effect on me or lactose intolerance for other folks) while not testing positive for a food allergy. You have do dig deeper.
The best way I've found to determine the cause of such things is to keep a daily health journal. For me, I tracked how I felt, how I slept, my weight, miscellaneous health notes, exercise and everything I ate or drank (including how much water). It took very little time for me to isolate grains (especially wheat) as the culprit in my acid reflux. It also resolved several other health problems for me. The bottom line, though, is simply track your data. Or, in this case, your son's data. Doctors cannot do this for you since they aren't there all the time. It's a tool that's not available to them, but an extremely powerful diagnostic tool that you can use for the cost of a pencil and a notebook.
You have tremendous power to study the problem personally and to greatly increase they probability of good medical outcomes for your son. Bringing your data and observations to his doctor may help zero in on underlying causes instead of the usual approach doctors have to take which are often simply trying new treatments until something works. Make yourself the key member of your son's medical team.
Life is short: Void the warranty.