I empathize with your situation as I am a chronic pouchitis sufferer. After a year with a jpouch the only real drug recommendation I can offer to help with pouchitis is what I have been on for over a year that seems to work wonders....augmentin. It is the strongest antibiotic out there and works like magic on my chronic pouchitis.
I moved to a GI about a two months ago as I felt I needed a doctor closer to me (my surgeon is in NY) and I moved past the surgical consult period. I also needed one who accepted insurance as my surgeon did not.
My GI, who is always thinking outside the box, recently started me on xifaxin with terrible results (pouchitis worsened). As others will tell you on the board, pouchitis is like a moving target and often many different drugs/regimes are tried..some with success..others not so much. I also have chronic fatigue and muscle aches with joint pain that I am being told goes part and parcel with IBD, but is also a manifestation of pouchitis.
At some point, your surgeon usually feels his job is complete unless you need additional surgical intervention. Mine helped me for the first 6-8 months as he promised he would help console me through the surgery and adjustment period and he did. I had an incredible surgeon with no surgical complications except for a minor stricture that worked itself out over time. My ostomy scar is amazing. I was so lucky and thankful that I chose such a skilled surgeon, and yet I have had chronic pouchitis and cuffitis over the last year, nothing which can be contributed to the fault of my surgeon. I just happen to be one of the less fortunate jpouchers and sometimes I wonder if having the disease for an extended period of time, as I did (23 years), may increase your odds of developing pouchitis more so than those who have surgery earlier in their disease...just a guess on my part.