Has he been tested for Heliobacter Pylori??
I know of several people who have been tested recently & confirmed this as true diagnosis for GERD/IBS symptoms - myself included - its curable with specific anti b's :)
in Adults its a blood test, not sure in Kids, might be stool test, but blood test more accurate apparently
My own DD has some problems with this too, not yet tested as only found out my own today - but reading up it can be passed on, so its more than a possibility
DD has food additive intolerances, & lactose intolerance, she can be dairy & wheat intolerant during a flare up - (flare up been diareah, stomach pain, & gerd symptoms) she can eat diary & wheat otherwise, but not in large amounts
Have you tried Viridian stomach flora?? this helped DD