Molly, If the doc doesn't think these symptoms are related what does she think is causing them? If she isn't offering any treatment for these "unrelated" symptoms I would find another doctor. Has she had an ultrasound?
When I have ovarian cysts I have pain on that side that varies from dull pain to a pinching of the ovary with intermitant stabbing pain. I had a laproscopy many years ago to remove one cyst that was a fluid filled cyst. The doc said that I would get more of them and I have. They frighten me since both of my grandmothers died from ovarian cancer.