I was also diagnosed with chronic pouchitis right out of the gate. My first course of antibiotics was 6 weeks after reversal. Kept trying 2-3 weeks on antibiotics and tried to get off, but as soon as I'd stop, symptoms would return.
So, currently, I rotate Xifaxan, Flagyl, and Alinia. Usually on each for maybe 3 weeks at a time. Been using these for a few years now and still all work well.
I didn't understand antibiotic rotation, and no one really told me about it at first, so I was on the Cipro for 6 months straight after my reversal. This one no longer works for me. Then, I switched to Augmentin, and I got pregnant right after I started. Augmentin was the recommended antibiotic to be on for my entire pregnancy and during nursing. So I was on this for about 15 months. After 15 months, it completely stopped working, so I decided to switch to stop nursing so I could get onto something else.
I read about Pepto Bismol on this site and how great that can work since it kind of works like an antibiotic. It was amazing. I was on that for maybe a year but again, it didn't click with me that I probably should have used that in rotation. This one also no longer is effective for me.
That's what I know for now! Rotation is key. If you start off doing it right, you can probably keep them going for a very long time. Don't stay on anyone too long. We still have several antibiotics lined up for me if I should need them to use in the rotation, but for now, I'll stick to these three.
Like Scott, have been doing this for awhile, so let me know any other questions you have.