Make sure you get a second opinion before you have any sort of surgery!!! Have you had a laperoscopy for your endo before?
You can have your period and still have PCOS. Everyone is totally different in their symptoms! There are diseases that have similar symptoms and a responsible doctor will test for those before making a Dx of PCOS. It sounds like your Gyn isn't interested in testing for those since they aren't gyn related. I would go to your primary care physician and talk with her about your symptoms and concerns. Was your testosterone tested?
My right ovary is enlarged, always has been, never has been a concern for me, but I have had second opinions so I know it is ok. Please, before anyone cuts into your body, get a second opinion and spend hours on line researching alternatives.
Spend some time on this site researching PCOS and build a sheet to take to your primary doctor with your concerns, symptoms & goals.
I'm not sure I understand what a sore uterus is... probably because I haven't experienced it, didn't know it could get sore. Sorry you are uncomfortable! If it is endo, is it possible to have it lasered off? There is a Endo forum on the board, you can find it here:
Endometriosis