I think you are on the right track, focusing on healing your gut. I've heard good things about fecal transplants. I would suggest starting with prebiotics in the form of potato starch and cooked and cooled rice. Check out the thread on resistant starch and of course probiotics too.
Here is somehting else to consider. Personally I would do this before ever considering surgery:
Trichuris suis therapy for active ulcerativ... [Gastroenterology. 2005] - PubMed - NCBI
For the Good of the Gut: Can Parasitic Worms Treat Autoimmune Diseases? - Scientific American
Life is death. We all take turns. It's sacred to eat during our turn and be eaten when our turn is over. RichMahogany.