Disparity between doctor's opinion/endoscopy and pathology report

"Chronic Pouchitis" from the pathologist's point of view isn't the same as what's visible, and it especially isn't necessarily the same as what you experience. Have you had any pouchitis treatment? Have you ever gotten your pouch into what felt like a healthy state, at least for a few days?

If I couldn't get a good night's sleep I'd try a course of Cipro, regardless of how the pouch looked. But I don't get (or at least haven't gotten) any major side effects from most antibiotics.

I tried Cipro and flagyl for 2 weeks, they made things better for a week but symptoms came back quickly. It also caused me bad thrush. That was probably the best my pouch ever felt. I went two nights without waking for a BM.

Symptoms are in many ways similar to UC in my experience

As soon as I start any antibiotic I also take Align daily.......a probiotic.  It works for me......no thrush, etc.

In my opinion combining antibiotics should be reserved for when all else fails. It doubles the side effect exposure and isn't necessary for most people. I'm now on both Cipro and Flagyl, but I was able to avoid it for years. Similarly, it's important to find the lowest effective dose, to minimize side effects.