Dang I thought I suffer with chronic pouchitis but what you went through is so much worse
I have no advice because your situation is the most severe I've seen. I know for me, my auto immune disease redirected itself to my joints and my pouch. I'm on azathioprine again because my auto immune disease did not get removed with the colon. It just found other targets in my body
Also I'm taking probiotics 4 times a day but it's never as good as cipro. I actually had formed stool on cipro and I'm never able to achieve that without.