Hi Doug,
I'm sorry to hear all you are going through and having to navigate a new diagnosis to boot, ugh. I would work to try to get some kind of consensus with a GI/surgical team (and the specialist treating your new autoimmune disease?), even if it means second opinions, these are big questions to consider and you deserve all the information to make an informed decision. You can always try the J pouch and go back to an ostomy, wheras an end-ileo is permanent. It might be worth trying the J pouch as you'd have a bit more bowel being used, plus a reservoir, so your output may not be quite as bad as your ileo.
To answer your question number one....I just went through this with my surgeon as I diverted my J pouch to a loop ileo. She said "at some point" the J pouch would need to come out if i opt to keep my stoma, but said we're talking years, not months. My understanding was that it can stay in there for a while as long as it is scoped regularly to keep an eye on it....of course ask your physicians, but this was what I was told just last month. My J pouch is 20 years old so i don't know if that makes a difference.
All the best to you!