I assume you have (or will have) another temporary ileostomy? In that case, yes, I imagine you would still have mucous and blood coming out of your pouch. That's a good sign, it means the tissue is healthy so don't fear it. If you had a permanent end ileostomy (meaning you are having your j-pouch removed) the anal area would be sewn shut and you would have no mucous or blood passing thru. The adaption to the j-pouch can be frustrating so be patient with the process. Most likely you will experience some urgency and discomfort in the first few weeks. Frequency will be higher too. Expect to see improvement in six week increments. Recovery is two steps forward and one step backwards for about the first year. It's not all bad, you will be healthy and will have the opportunity to put weight on and get your stamina back. But the new plumbing has to learn how to behave like a colon and that takes time. Please check into www.j-pouch.org if you get frustrated or down. There are a lot of people on that board who can provide you with support and share their experiences. That board got me through my first year and I learned that I was sharing some of the same recovery issues as others, it made me feel okay. My surgery was six years ago and I am fat and healthy six years later! You will be healthy again soon too.
It sounds like you have been through the ringer but should be in very good hands at the Mayo. Continue to get well, I will send good thoughts your way.
Yes, I had rectal physical therapy after my takedown! My sphincters were traumatized from the surgery so my surgeon sent me to his rectal PT. She was a godsend and the exercises she prescribed cured the bit of incontinence I had in the few first months post surgery. Again, it sounds like you are getting excellent care.