Incomplete or difficult evacuation was, for me, a hallmark symptom of pouchitis. My initial bout of pouchitis was around 2 years after takedown. In regards to treatment, the pregnancy complicates matters. Not sure if antibiotics like cipro or flagyl can be taken by pregnant women. I am sure there are others here who can opine on that.
I think you need to see/establish a new GI and get it treated in some manner and have it nipped in the bud. Good luck!