I had this problem after the jpouch surgery (stage 2) and also at reversal (step 3)
after my j pouch surgery I suffered urinary retention and had to self catheterise for a few weeks. my surgeon didn't know why this was happening and neither did the urologist but it cleared up and I was able to pee normally again.
recently I had the reversal and again I found it hard to pee. I think, in my case, its due to the pelvic floor seizing up from the trauma of the surgery and then at takedown because the muscles hadn't been used in so long.
I had to get my pelvic floor to relax and then it all flows fine.
I did this partly by squatting over the toilet and peeing, and what I found helped the most was getting a hand held bidet spray and whilst cleaning the behind, it seemed to relax everything and I could pee.
http://www.amazon.co.uk/Panaso...P300-A/dp/B00ECVA7SI