I'm not sure how much I can help you but I want to reply. I have had epilepsy for the past 9 years. I was diagnosed with Asperger's Syndrome (on the autism spectrum but high functioning) last April but probably have always had it.
I don't know about behavior problems from either of the conditions (except for the meltdowns associated with Autism/Autism spectrum disorders) but those of us on the spectrum react differently to medicines than people off the spectrum. As a general rule anyway. I am lucky in that all I do is become tolerant of medicines very quickly. I think some people react the opposite of the way the medicine is supposed to affect them.
As far as not wanting to be touched-has he alwasy felt that way about that? I have. I hate it. I can handle hugs and things from certain people and from family without too much of a problem but to me, and to some others on the spectrum, being touched is very intense. I hate it when people come up and put their hand on my shoulder or waist as they say hi. And I don't do eye contact either.
Good luck to both you and your son. I hope you can find answers that require the least medicine possible.