Whatever you have now, it isn't gonorrhea, chlamydia, or any other STD. Your original symptoms (burning sensation) were consistent with STD but not typical; discharge is the main symptom and penile/urinary burning rarely occur by themselves. Anyway, the test results were reliable, regardless of how long since you had urinated--so most likely never had any infection at all. Your urologist seems to be 'reaching' for possible infectious explanations and treating you for every conceivable possibility, but the lack of response to the various antibiotics is further proof of no ongoing infection. That your partner apparently had a normal exam (and presumably negative STD testing?) also reinforces the same conclusion.
Your sypmtoms are most consistent with male pelvic pain sydrome, the newer term for what used to be called chronic nonbacterial prostatitis. (True prostatitis is rare in younger men.) The syndrome is probably due primarily to increased pelvic muscle tension, related in turn to anxiety. I cannot comment on the appearance of your centrifuged urine. A few RBCs from time to time often is meaningless, and you don't comment on white blood cells--which suggests that the white pellet isn't pus or inflammatory cells. It could be just phosphate crystals, which are normal depending on diet and urine pH.
I suggest you re-check with your urologist about the results of your self-urinalysis. But I'm betting you have no infection at all. And if you do, it isn't an STD and it isn't anything you caught from the sexual exposure 3 months ago.
Good luck-- HHH, MD
By the way, I have never had any discharge or even a hint of fever. Also, I had been off antibiotics for a month before I had the last GC/CT test. Before I went to the urologist I had been taking cranberry extract capsules up to 3 days before my appointment which cleared my urine and made the burning sensation go away. It also diminished the pelvic pain about 50%. I explained this to the uro. He only did a dipstick test on my urine (or at least he charged my HMO for it). The symptoms came back about 1 hour after he did the DRE (cloudy urine and burning), then subsided for a couple of days after I took the flagyl. My gf went to her gyn for something unrelated and got a pelvic exam and wet mount. He said everything was "normal" so I assume no cervicitis, vaginitis, or trich. Just thought this additional info would be useful but couldn't include it above