I'm not going to be able to provide the clear answers you are hoping for. Generally that's impossible when several providers have been involved; distant adivce from an online source, no matter how expert, generally is less definitive than driect exam.
Your symptoms are not typical for NGU and never were. First, the dominant symptom is discharge, with little or no dysuria (uncomfortable urination). Second, the incubation period was very short; it's usually 7-14 days or even longer. Third, NGU almost always responds to the treatments you were given. When the problem persists or relapes, it's generally that symptoms clear up and later return, not continued symptoms despite antibiotics.
Your "trich" (trichomonas) idea might have merit. It is the only infectious explanation I know of that would not respond to the drugs you have taken. But all the atypical features above still apply, about the nature of symptoms etc. So I doubt trich is the problem, but you probably should ask your doc about it and consider a course of appropriate treatment. The newer drug tinidazole (Tindamax) probably is more reliable in men than the old standard, metronidazole (Flagyl and generic brands). But don't get your hopes up.
All things considered, my bet is you have the male chronic pelvic pain syndrome. CPPS used to be considered a form of chronic nonbacterial prostatits, but the prostate itself probably isn't usually involved at all. CPPS is increasingly believed to be the result of heightened pelvic muscle tension, often anxiety-related, which can cause a whole variety of symptoms, mostly similar to yours. Fortunately, it appears to be a problem of comfort only, i.e. without threat of any serious outcome. You can find loads of information if you google "chronic pelvic pain syndrome". I suggest starting with the Wikipedia article; although Wikipedia can be spotty, the CPPS article is excellent. Then discuss it with your urologist or other provider.
In summary, except for the slight possibility of trich, you an be sure you have no STD. In all probability you have nothing that will ever harm you or a future sex partner. For some men with similar symptoms, just knowing that is the starting point of recovery. Most people can live with a little discomfort if they know it's nothing serious, just as people live with chronic back pain or any number of other minor ailments.
Good luck-- HHH, MD
Can "trich" go away on its own if Tindamax doesn't work? Or, does it usually kill the parasite, assuming that were the problem? And, when is it again safe to have unprotected in a monogamous sex without infecting a partner?
No STD causes prostatitis (well, gonorrhea, but so rarely that I have never seen a case in 30+ years in the STD business). Whether or not you had overt prostatitis, as your urologist thought, or CPPS, it wasn't due to STD.
I already said you have nothing that will ever harm a sex partner. If you wan't to be double sure, have the trich treatment. Aside from that, unprotected sex is fine; you have nothing to transmit to a partner.
Further note: some of the sites for CPPS look like scam website or herbal drugs, etc? The wikipedia one was better...
Also:
http://findarticles.com/p/articles/mi_m3225/is_n2_v39/ai_7553271
http://www.chronicprostatitis.com/nickel.html
“A number of observations support an association between Trichomonas vaginalis and prostatitis.[71-74] In one study, the prevalence of Trichomonas exceeded 85% in men who had symptoms of prostatitis that persisted despite their receiving antibacterial therapy.[75]”