Hey Sally,
It always takes me a good 10-14 days to fully recover from a cystoscopy, but 2 months (June to now) is awfully long. When you say the urine is clear, do you mean a urinalysis or culture? If a UA is clear but you haven't had a culture, you need a culture. If a culture was negative, you need to know that the UA is clear as well, because, if not, it could point in a direction worth investigating. Finally, consider that the symptoms of vaginitis are not always easily distinguishable from urinary symptoms.
But my final answer, is you might not be able to figure this out yourself, so since this has been going on so long and started with the cystoscopy, give your urologist a call.
