I'm always worried about what ovary problems may pop up, and how they might affect transition. I haven't been diagnosed by a dr. with PCOS, but I have enough symptoms to be diagnosed without actually having cysts on my ovaries. Still, the fact that I've never been checked for cysts before worries me. I basically have no idea what's going on in there. :/
Were there any other symptoms, such as pain? Since I stopped taking female hormones, I've been getting on and off pains from my ovaries, completely unrelated to my cycle (which, has basically stopped as well). As a poor person (and by poor, I mean VERY poor), I try to avoid unnecessary doctor visits as much as possible, but for something internal like that, it's hard to tell when it really is time to see someone about it.
I have a cyst on my spine, by the tailbone. It was so huge and painful by the time I went to have it drained that I couldn't even lie on the hospital bed. After that horrible incident and my experience at that particular hospital (they didn't numb me properly so I felt them slicing me open with a scalpel), it makes me worried thinking about ovarian cysts that might be down there.
Good luck to you. I hope all goes well.