No, a cystoscopy looks for problems with your bladder, urethra and prostate. NGU is diagnosed by looking for white blood cells or bacteria in your urine.
I know you had gon and chlamydia testing done, but has anyone mentioned looking for white blood cells?
Did all this stem from the encounter you had in Aug? Are you unable to let that go?
It sounds really simplistic, but male sure you are drinking enough water, and lay off the caffeine, alcohol, sports drinks and juices. Those are all really irritating to the bladder and urethra, which could be causing the pain you feel.