I don't want to bash your beliefs, but I read the GAPSdiet.com FAQ -- it's very, very long -- and want to warn anyone reading this thread that there is no scientific evidence to support this claim or any of the claims made by Natasha Campbell-McBride (the creator of GAPS). Nearly all of her claims are bizarre and flat-out wrong, and she hasn't produced any studies in support of them.

While the gut is related to a lot of illnesses (read the New Yorker article called "The Excrement Experiment"; it's about fecal bacteriotherapy), the GAPS diet is based on thoroughly discredited claims, including:
1) electromagnetic radiation damages mitochondria;
2) autoimmune issues stem from the gut;
3) coffee enemas are good for you;
4) microbial exotoxins with masses of over 4000 Daltons damage your brain after passing through the blood-brain barrier (in reality, nothing larger than 500 Daltons can pass through it);
5) non-organic food items lack nutritional value;
6) sitting in a sauna removes toxins;
7) whatever is in the mother's blood will be in her milk ( nope);
8) vaccines can cause autism (huge red flag here);
9) homeopathy isn't quackery (biggest red flag).

The list goes on and on. She also has a lot of stuff she would love to sell.

In general, if something says it will help with "detoxification" or makes bold, entirely unsubstantiated claims about miracle cures of autism and other illnesses, then I assume it's a hoax. If something claims to be a cure-all, then I assume it probably cures nothing.