Have you tried an elimination diet under the supervision of a doctor? There are lots of kids on this forum who have different intolerances and allergies. I usually recommend trying to pinpoint exactly what is going on before trying treatment.
For instance, I just read where, although gluten-free diets have become popular, only a small portion of people have celiac disease - but there are many people who are allergic to or intolerant of wheat. If it's just wheat, you don't need to go gluten-free: you can simply eliminate wheat from your child's diet. (This means rye, oats and barley and flours and wheat-free flours and breads made from them are OK) You would have to make that judgement with the help of a doctor, though.
My child is lactose intolerant, which seems to be another common culprit. We were dairy-free while I was nursing and while he was small. He developed an ability to tolerate processed or cooked milk products, so the only thing we avoid these days is liquid milk (for some reason, we still get stomachaches from UHP lactose-free milk, which is essentially cooked and has an added enzyme that processes the lactose - but we just use Almond milk instead.)
I am wary of supplementation - I think first and foremost, your goal should be to do no harm. It's worth a try if properly managed - and I admit, we do a fish oil/multivitamin combo as recommended by our physician. However, I also know that there doesn't seem to be good science behind either one. http://www.autismsciencefoundation.org/ ... treatments http://www.nature.com/news/fish-oil-sup ... ky-1.11484