I also had recurring pouchitis symptoms like yours, but also with increased frequency and abdominal pain. For 19 years pouchitis was infrequent until last fall. A scope revealed pretty severe pouchitis and I went back on Flagyl, but at a higher dose. Fine while on antibiotics, but symptoms would creep back after a couple of weeks of the end of the course. I also was taking Align, but stopped it, since it did not seem to be helping. I used Canasa suppositories for about 5 days when I felt the symptoms coming back, plus I started taking a multistrain probiotic (Nexabiotic) to switch things up. Things are more stable now, but it may also be because I changed my biologic from Humira to Cimzia in December because the Humira was not controlling my arthritis well anymore. If that did not work, my GI was infavor of my rheumy adding methotrexate or Imuran to the regime.
Another strategy I have been working on is reducing my carb intake. Since my husband and I have type 2 diabetes, this was necessary anyway. It seems to help too.
Jan 