I'll give my 2 cents on this, although thankfully I never had to personally deal with this, but know people who have.
While diet and drugs make a difference, and as much as I push nutrients and eschew drugs, I fear the problem goes deeper. The ladies and I were mentioning this at bible study. It goes back a generation or two with the foods, medications, injections, etc that are basically changing the genetics of the parents and giving offspring with these types of issues. For example, have you ever heard of so many kids with peanut allergies as there are today? Heck, in my day, a peanut butter and jelly sandwich was a kids' staple -- we all had them in our lunches. Now half the kids can't eat them, and heaven forbid if we serve a pack of peanuts on an airplane.
Yet, nobody asks the question why this sudden increase? Same with autism, and the same with other childhood medical issues. I know of a case in our church where the boy had such issues, and the mother herself, at only 40 (generation x) was diagnosed with melanoma. Kind of supports that theory of the genetics being messed up. I never (as a kid) remember people that young getting that sort of stuff.
Now for some more pragmatic information. I heard various reasons for kids with autistism including the mother being diabetic (more of that these days), iodine deficiency, vitamin D deficiency (we are told to take our cholesterol pills and stay out of the sun -- since cholesterol is basically vitamin D, people who do that tend to be vitamin D deficient which can cause heart problems, depression, diabetes, etc). All this was probably brought on with our famous highly processed diet. Generation X on down to Y and soon, Z are probably the most overly-medicated generations. And these are the generations where the DNA damage seems to be starting. I never saw so many young people almost half my age on pills.
The bad news is that if there's genetic damage, then diet and natural methods will only go so far and be supportive to minimize the problem. As much as I hate to admit it, some medications may be in order, but be careful. This is a case instead for guided mega-vitamin therapy for sure. Not the do-nothing Centrums A-Zinc multi-vit nonsense. They are basically worthless (and then doctors say vitamins don't work; no wonder with those small dosages).
Wish you the best, and do some research along the lines I mentioned. It may greatly alleviate this, along with faith can do wonders.