I had my pouchoscopy already today. Whole pouch was clearly inflammed and ulcerated. Small intestine looked apparently normal so thats good news, although they of course see only the small part at the end. Regarding my not-so-typical general symptoms, the plan is to check if the situation improves as the pouch starts to heal and if not, then have an gastroscopy.
I was prescribed a 4 week course of Cipro. I've been avoiding Cipro and managed to deal with the pouchitis symptoms with Flagyl / metro in the past. I've been very anxious about the side-effects and possibility of tendon ruptures from Cipro. But I guess I dont have any option at this point.