Although symptoms like you describe might from time to time be the only symptom of genital herpes, the large majority of those with symptomatic initial HSV infection get cutaneous genital lesions. The reports of such symptoms are entirely in retrospect: that is, some people who are newly seropositive and/or exposed to a person known to have genital herpes recall symptoms like yours. But whether those instances were causal or coincidental isn't clear. I have never seen a case like yours that turned out to be herpes; and in general, herpetic urethritis isn't subtle--some men describe it as the worst pain they have ever experienced. And most of those cases are associated with obvious external herpetic lesions. More briefly, herpes rarely explains the mild sort of symptoms you describe.
The persistence of your symptoms after treatment with ciprofloxacin and azithromcyin is a strong indication that they are not due to chlamydia, gonorrhea, or any other bacterial infection. I doubt your non-urethral symptoms are connected at all, unless you have some yeast overgrowth as a result of the antibiotic therapy.
So what is it? Speculation tends to center around chemical or allergic irriration (e.g., reaction to a vaginal hygiene product, spermicide, or the latex of condoms); or on emotional issues (I often surmise that anxiety magnifies otherwise normal body sensations). But those are quite unsatisfactory, at least to me; and the bottom line is that nobody really knows what is going on. But most important, there is no evidence that this syndrome--whatever is causing it--leads to any long term health problem either for the affected patient or his future sex partners.
Bottom line? Of course, check with your own health care provider (a real doc, not just a med school buddy) if your symptoms persist and are bothersome. (There likely is someone on the faculty at your med school who is pretty sharp on STDs.) Or just sit tight, with the expecation that they will fade with time and that they are unlikely to reflect any ongoing infection of importance.
Good luck-- HHH, MD
thanks for taking the time to give me some context for the symptoms I've had. I'm not one to worry needlessly once the docs have given me their opinons...
regards, SMS