Hi Megan. First, best of luck to you if/when you do try to conceive! I have chronic pouchitis so I was on Augmentin to treat that my entire pregnancy. If you just have random bouts of pouchitis, you can take Flagyl no problem 2nd and 3rd trimesters. I think 1st trimester, if needed, you'd likely be prescribed Augmentin. I didn't take any bowel slowers during pregnancy for 2 reasons. First, your digestion will slow down a lot in the first trimester. I was only going once a day sometimes. Secondly, since I was on antibiotics the entire time, that helped reduce the frequency and thickened everything up. The last few weeks, there is significant pressure on the pouch so frequency will pick up. I don't think I took anything other than Unisom to help me sleep through the urges so I wasn't up every 1-2 hours in the bathroom. I never had any leakage issues. Just once a few hours after my son was born since I was so numb from the epidural, I didn't realize I went to the bathroom :/
As for adhesions, they did not affect our ability to conceive, although they do for many. We conceived 6 months after my takedown, our first month trying. I recently learned that I have/had a lot of adhesions since I just had surgery, but none affected my reproductive parts. Just caused me bowel obstructions (not during pregnancy, but a few years later).
If you have any other questions, I'd be happy to answer them!