"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.