Your situation sounds almost identical to mine except that I was experiencing symptoms sooner following the jpouch surgery. I too was hopeful about the Bartholin's cyst but after marsupialization (?) the symptoms continued. I eventually got an MRI which confirmed two fistulas from the pouch - one to the vagina and the other seeming to go nowhere. It was thought that I had an undetected leak following the j pouch procedure which caused the fistulas.
I had a flap advancement surgery to try to close it off. Within a week it was apparent that it hadn't worked so I had a diverting loop ileostomy a few weeks later to try to let it heal with 'no activity down there'. I had to have a couple of ileostomy revisions and during one of those surgeries a second flap was performed. Ten months later the jpouch was attached as an investigation under anesthetic showed it had closed. However, I was disappointed (devastated) to say that it hadn't closed and stool is draining into the vagina. It also appears that the second one is also active now.
So, the questions of the surgeon are: do I have Crohn's even though every thing else points to a continued diagnosis of UC. Or, perhaps there is a branch(es) not showing up and the flap is not is the correct place.
Anyway, the plan is now to try a trial of Humira to see if they will close (thus, yes it's Crohn's) or if they don't heal I will have a permanent ileostomy.
This is not to say that your situation would be the same. Yours may well heal and the ostomy is unnecessary or, at worst temporary. I too had ongoing hell with my ostomy. I'm told that loop ileostomies are more prone to problems so I'm hoping that an end would not be so problematic if that is indeed the route it has to go. I'm sure hoping that I don't go back to the ostomy but I'm not too keen on a new Crohn's diagnosis and being on Humira indefinitely. But again, yours may be one of the many that do heal with the surgery. I felt I had to try the flap at least and also I have to try the Humira as I don't want any more surgery and nor do I want to return to the bag.
I would offer to send you luck but seems I don't have a lot of that. So I'll send you love instead.....