I agree that the first step is to get in touch with a DAN! doctor. Even if you don't end up sticking with one (we didn't), they can run run a variety of lab tests that can narrow down your son's individual issues (ex: heavy metals, vitamin and mineral deficiencies, parasitic overgrowth, etc). There's no single course of treatment because each child is different.
DS suffered vax injury at 7 months. We see a DAN! doctor and also contacted the NVIC for advice. DS has recovered completely from his neurological injuries, which involved moderate-severe autistic-like behaviors and pituitary injury. He regresses during fever illnesses and diet changes, but he recovers.
Wife to Chris 12/27/07. DS1 Earth Day 2009 (4/22). DS2 March 6th, 2012.