There are many avenues that I think you can take with dealing with AS and the gut. It might be helpful to find a DAN! doctor. I believe there is a link on The Gluten File.
Also, you might want to check out digestive enzymes:
http://www.enzymestuff.com/index.htm
For me, testing for delayed food sensitivities (IgG antibodies - it's a blood test) was very helpful to figure out what to eat and not to eat. Even though my doctors were skeptical of the accurracy of the results, I avoided the foods I was reacting to, and I feel better. Of course, the foods I have been avoiding, like gluten, corn, and dairy, did not show up at all as any kind of reaction. That's to be expected, because the body won't produce antibodies to these foods after a while.
There is tons of links on this website from a mother of children with autism. She has links on AS as well. The amount of information on here might be overwhelming, but you might find something of use:
http://www.danasview.net/index.htm
I researched these websites for my own information because my nephew has Asperger's Syndrome. I figure we share similar genes.
Claire