Your symptoms don't suggest herpes at all. They really don't suggest any STD, and most possible STDs would have responded to the antibiotics you received. Don't worry about syphilis; both ceftriaxone (which probably was what the injection was) and doxycycline would have cured incubating syphilis before it got started, so there is no point in being tested for syphilis. Your HIV test result has already disproved that possibility. You could get tested for herpes if you like, but even if positive, I will be 100% convinced it has nothing to do with your symptoms. (A quarter of the US population have positive blood tests for HSV-2. Think carefully whether you really want to be tested for it.)
For what it's worth, I also doubt you had epididymitis, which does not cause the mild, vague symptoms you describe. Epididymitis causes excrutiating pain of a single testicle, usually with dramatic tenderness to the lightest touch. (Epididymitis sometimes is suspect in men as arrive at the door to an STD clinic, because of the way they walk!)
AS to trichomonas, it almost always is asymptomatic in men, and it's hard to diagnose in men. On the other hand, a trial of treatment is easy, just a single dose of the antibiotic tinidazole (Tindamax). (Tinidazole is new in the US, but appears to be much more reliable as single dose treatment for men than the older treatment, metronidazole [Flagyl].) So you could discuss this with your doctor. But it won't resolve your symptoms.
My main advice is to just sit tight and do nothing. Your symptoms probably will fade with time. Whatever is causing them, you can be certain it is nothing that will ever cause you any kind of serious health problem, and nothing you can ever transmit to a future sex partner. Anxiety alone is a very good bet.
Good luck-- HHH, MD
HHH, MD