To add to the great tips that other members have posted here -
Try eliminating all grains, sugar and anti-nutrients from the diet; eliminate A1 diary; eliminate beans and legumes and even nuts (can re-introduce them later if needed). Also try to hit a low-carb, high-fat, moderate-protein composition in his diet.
A healthy gut is important for the immune system. Also try to achieve ketogenic state in the kid, so that his brain function is optimal. Ketogenic diets (think coconut oil) have long been used against epilepsy and is now also found useful against Autism, depression and many other gut-brain issues - https://en.wikipedia.org/wiki/Ketogenic_diet#Other_applications
Good luck to your son. Food is medicine and we should take full advantage of it :)