Yes, this happens because there is no definitive test to rule Crohns out. My own GI felt I had Crohn's but my surgeon thought otherwise and pathology on the colon after surgery indicated UC. Does that protect me? No it does not. If you have Crohn's-colitis you are still a good candidate for a j-pouch. If you have CD you are not. To answer your questions:
1. In my opinion, yes if you have dysplasia the colon should come out regardless of your IBD diagnosis. There are many who would argue that dysplasia can be misdiagnosed. I'm not much of a risk taker so that would be enough to sent me to the OR.
2. If it is CD your surgeon will not perform a j-pouch but will do a permanent ileo.
3. That's a choice you have to make. There are several CD j-pouchers on the board who are managing their CD quite well with a j-pouch and have no current plans to have additional surgery.
4. There is no science that can accurately determine which disease you have. My surgeon (one of the best CR surgeons in the country, a researcher, and a doctor who has performed over 2000 j-pouches) would be the first to toss out the Prometheus tests. He was able to show me how their testing procedures were flawed. In my case the PANCA results indicated I would have chronic pouchitis, my surgeon said that was not so and in 7 years with a j-pouch I have never had pouchitis.
I think your next step is to consult with a top CR surgeon and pose these questions to him or her. You are obviously well read on the subject and are ready for a informed discussion on the pros and cons of your situation. Ask your surgeon if he/she has any pouch patients who were later diagnosed with CD. Ask your surgeon for references of his/her patients to talk or meet with.
dx proctitis in 1987
dx UC in 1991, was stable until 1998
1998 started prednisone, asacol, pentasa, nortriptylene, ativan, 6MP, rowasa enemas and suppositories, hydrocortisone enemas, tried the SCD diet, being a vegetarian, omega 3s, flax, pranic healing, yoga, acupuncture, probiotics
2000 lost all my B-12 stores and became anemic
2001 opted for j-pouch surgery- now living life med-free