I had never heard abdominal, flank and lower back pain being caused by PCOS. If that is the case, maybe I am not getting the pain from the kidney stones like i thought. Lately I have been having a lot of pelvic pain, abdominal pain, lower back pain, and flank pain on both sides, and the doctors have been debating whether it was my kidney stones causing it (as the kidney stones are still in the kidneys on both sides). I have PCOS, and have for about 2 years. My periods are so painful. I just want to cry all of the time.
I would ask the doctor to test you with lab results that show PCOS. I can't remember what they are. PCOS also causes some people to have impaired glucose tolerance. I ended up getting diabetes. Birth control can help with some of the symptoms. Maybe you should try that. It doesn't seem to be helping my pain though.
Sorry that I can't offer much help. Hope it starts getting better.