First off, let me say that I have walked in your shoes, and still am!
Things really came to a head with my daughter when she was 4. That is when I realized that she wasn't the typical hyper kid. By 5, I had done enough research online to realize that it was probably food allergies, but all of the blood testing and the scratch tests we had done at the allergist had ruled out everything- they showed that she was allergic to nothing, yet she was still stuffy a lot too and we finally took out her tonsils, which still helped nothing.
I finally, feeling overwhelmed and not knowing where to start, removed red 40 after realizing that the snowcones we were going to get on Fridays (as a treat if she had had a good week at preschool) were making her behavior really atrocious that night. I took her off of red for 2 years and it was a lifesaver. It took about 2 months to COMPLETELY get it out of her system (beware, the strangest things have colors- bread, frozen meals, bbq sauce...) and then realized that yellow 5 seemed to affect her as well, so we removed ALL coloring from all the foods that enter our home and her mouth.
Still, a year or so later, she was obviously reacting to things, and I did some research and just this past summer found the Feingold diet, which has truly truly turned her life around. She reacts VERY strongly to apples (as we have tried to re-introduce foods now.) We have also started therapy (which it sounds like you probably do since you have a diagnosis) and she also has SPD, OCD, and was recently diagnosed with Tourette's Syndrome. My daughter turned 8 in Sept, if you are wondering, so this has been a lifelong process in trying to tweak her diet and figure out the association between what she eats and what behavior changes it causes.
I commend you for posting, and for doing research and caring what goes into your son's diet. It really is overwhelming and a huge struggle at first as you have to monitor every little bite and every thing you buy when you shop, but believe me when I say it is SO worth it. Imagine not struggling with the aggression (the biting, the hitting, the kicking, the scratching, the screaming) and being able to do a "normal" trip to the park or whatever. Diet changes have really allowed us to do that, and I never ever thought we would.
If you have any questions, you're welcome to contact me.
You can find info on the Feingold diet at: www.feingold.org. There are tons of stories on there just like ours.
And don't feel bad about not knowing- our society ENCOURAGES us to eat things that aren't even really food, much less good for us. The important thing is to stop once you know it.
Oh, also wanted to add this- dont' rule out something at school- could it be something new like brighter lights, new carpet smell, shoes that feel too tight suddenly, a change in where he naps/rests, a change in their routine, different handsoap or cleaning supplies, etc etc.