First, we are just never prepared for how hard this transition is. Hold on it gets better.
Some other things to consider: pouchitis can be fed by bacteria: So avoiding sugars, dairy (including yogurt) and gluten can really help. Take O'hhirra's (green box) probiotic, 2 of them 3 times a day. Don't take this at the same time you take your antibiotics. After you come off the anitbiotics, continue doing this for at least a week to a week an a half and then taper off to 1 or 2 a day. Remember that Cipro can cause serious joint problems, so watch for that, they can change you to Flagyl if you need.
Second, you need to **really** look at your stress levels.This surgery, illness and pain causes serious stress by itself and that is hard to manage because it is effectively an assault on your body. Our bodies are the canary in the coal mine and we need to listen to them. This means doing things that move your body out of fight or flight mode so it can get to the business of healing. This will lower your inflammation levels in your body.
This can be things like: star gazing at night, watching sun rises and sunsets:, bee watching, drinking a favorite herbal tea on purpose, sunbathing in the morning or evening for 20 minutes, turning down all the lights, pick some favorite music that is calming (I like Coyote Oldman and Jazz), going to the hot tub for 10-30 minutes in the evenings to unwind your body, get a feel good massage or a really good foot massage. Take a small walk with your dog or a good friend, or just by yourself to "explore what changed since yesterday" in your neighborhood. Visit a park you haven't been to that you know has a bathroom so there is no underlying anxiety that you "might not be able to take care of yourself if you really need to go".
But most importantly, remember what you are experiencing right now is not your final destination. Do not give up hope and think this is where you will stay. Hold grace and compassion for the difficulty your body is doing during this very difficult transition and remind it that you are in this together and that this is just truck stop on the way to somewhere else. It took me probably 7 years before things really stabilized, but they didn't start doing it until I started actively doing the steps above. Before that I was just trying to "manage my body". I'm at 13 years now since my take down. You got this... it's going to get better!