Awesome post.
I don't buy into the into the Autoimmune thing - so I'd actually like to dig up some results that show the "disease" came back and attacked the transplanted small intestine or colon... and that it was Crohn's or Colitis again and NOT transplant rejection.
I'd like to dig out the literature on this actually if anyone has any. My money is on it not coming back lol... Unless someone can show different or post a study where the entire Colon or Small Bowel was replaced and Crohn's or Colitis struck again.
Here's an article on someone that had this done in the UK for Crohn's..
http://www.theguardian.com/lifeandstyle/2012/jul/01/bowel-transplant-let-me-live-againMy bet is GI's don't consider it cause you can get along fine without your colon, put a new one in and you risk rejection and further surgery - not return of the disease itself.