Dear Don,
Sorry for what sounds like a dilemma. It occurred to me that if the cysto was clear (that's what I understood from your post, right?) and cytology positive, that yes, you should be looking at the ureters and kidneys, brush biopsy, maybe? Have you had a FISH test to complement the cytology? Might be helpful as to if the cytology is correct or not. NMP/BladderChek is cheaper and simpler and can also be done in the office to double check cytology. If they refuse the FISH there are more diagnostics, both urine and otherwise (there are pages on the main site under 'newly dxed', diagnostic tools', 'urine markers')
I would also be hesitant to treat the bladder until you are sure that there is cancer there! otherwise, the ureters or kidney would the target and the approach would be different. So no, don't jump to conclusions without a solid diagnosis (and your doctor should be of the same mind, I'm sure).
I sympathise with your feeling of repeated violation. I don't have bladder cancer, my sister does. I have breast cancer and if I had to pick....I'd choose breast cancer over bladder. Those cystos-the thought of it- but then again, I'm very wimpy. Most people here never complain about them. But I'm glad my cancer was external, anyway.
Take care,
Wendy