Chris, my initial thoughts are to do whatever you can to save your j pouch.  This might entail having a consultation with a doctor who has lots of experience in dealing with pouch problems.  Once your j pouch is removed and your bottom sewn shut, there is no going back.  If you would list the problems you are having, others on this forum could offer suggestions.

In my case, recurrent high grade dysplasia  in the anal cuff and a malignant polyp made removal of my j pouch necessary.  I strongly did not want an end ileostomy with its associated issues and researched the two alternative procedures that avoid the need for an external bag: the k pouch and the BCIR.  I selected the BCIR and have had excellent results.  Although my surgeon was not able to use my j pouch in constructing the BCIR, there was sufficient small intestine to make the BCIR (less than 3 feet).  Although I lost 40 pounds after the operation, I have put most of it back on and now have to lose a few pounds after the holidays.  I have no issues with weakness and dehydration and I can participate in all the physical activities I enjoy.  I am told that I have sufficient small intestine left to make another pouch, in the very unlikely event that becomes necessary.  Please feel free to send me a PM if you have any question, and best of luck to you.

Bill

I have had two pouches, but some length taken from the small intestine each time.  I had a pouch redo from Dr. Remzi, and I'm doing well. I weighed as little as 160 when I was in between surgeries, but now at 190, feeling well.  I hope that helps!

I tried everything to save my j-pouch but my GI at the Mayo Clinic scheduled an appointment with a wonderful surgeon there. We all discussed my future and my not wanting it removed as Bill said above it is a major life decision. She first diverted from my j-pouch to a permanent ileostomy. My j-pouch didn’t settle down so I had it removed 7 months later. I am glad I made the decision in 2 steps as I found out the permanent ileostomy was 100% better than my temp one was. I am glad I had it removed as I feel better and no longer take 4 medications for it.

I suggest you get a second opinion. Maybe you already have done so. I was sent to the Mayo Clinic by my local GI as I had cuffitis and recurring c.diff infections. He said he was a generalist and I needed an IBD specialist.  My Mayo GI treated me for over 3 years before he scheduled the consultation with the surgeon. I ended up not only with chronic cuffitis but chronic pouchitis as well as recurring strictures that led to pelvic floor dysfunction.  It just would not respond and work right. 

If you have any other specific questions please ask away.  If you want to ask anything privately then send me a PM.