I agree with Johnny Apple Bomb---You're on the right track and going about it in the right way.
I'd also recommend you look into Neurofeedback as an additional adjunct for your son. I have seen numerous cases of Autism respond profoundly to this intervention---virtually normalizing kids in some cases...nearly always helping. It's well worth a try. Here's a link to a video description of what Neurofeeback is: http://www.eeginfo.com/win_video.html.
If you feel you're interested, you can go to http://www.eegdirectory.com
to find a practitioner near you.
Also, in case you're not already familiar with this (though I imagine you are...you sound reasonably saavy and well researched), check out this web site: http://www.gfcfdiet.com.
It's one more thing that can make a profound difference in your son.