You're really overreacting; all evidence is against herpes. The most important information you provide is that your FP thought your penile lesions were not herpes; you can be sure that the average family doc is very capable of recognizing herpes. Aside from the penile bumps, you describe no symptoms that suggest herpes. Almost certainly you are examining your penis too closely and noticing enitrely normal variations in penile skin--you describe nothing that sounds at all abnormal. The acyclovir therapy made no sense; my guess is that you insisted and talked your doc into the prescription--it's hard to imagine a responsible physician suggesting herpes therapy in such a situation.
The urinary symptoms you describe are consistent with STD, such as chlamydia or nongonococcal urethritis (NGU)--but not typical for those things, and I doubt you had them. Prostatitis sound unlikely as well, but I cannot comment further--depends on what your doc found on examination.
Based on your description of your partner's problem, that sounds more like herpes zoster (shingles) than HSV. But her doc could have done tests to tell the difference; if not, your partner could have a blood test for HSV-1 and -2. Even if it turns out to be HSV-2, it probably is not a new infection; although recurrent genital herpes can occur anywhere in the 'boxer shorts' area of the body, the first infection almost always involves the genitals or anal area. In other words, if she has genital area HSV, she didn't get it from you as a result of the sexual adventure you describe.
Bottom line: Follow your provider's advice, and the advice of your partner's dermatologist.
Good luck-- HHH, MD