You give a confusing history that, in many aspects, makes no sense. Having a long history of oral herpes due to HSV-1 makes it extremely unlikely you actually ever had genital herpes due to the same virus. If you caught the infection at both sites at the same time, it is possible. But prior infection with HSV-1 provides a high degree of immunity to new infection with HSV-1. Also, 'small white bumps' on the (fore?)head of the penis doesn't particularly suggest herpes. If a virus culture from the penis really showed HSV-1, I have to accept the possibility you are the rare exception to the rule--but I am skeptical of that report.
Second, surgery is not a normal treatment for epididymitis, certainly not for epididymitis due to infection. Further, no STD causes persistent or recurrent epididymitis; and if an STD was the cause, you would have had a positive test, most likely for chlamydia, less likely for gonorrhea.
Finally, you have seen at least one health care provider about your problems--apparently at least 2 urologists. If people with their expertise cannot come up with clear answers by direct examination and testing, certainly I cannot.
So to answer your direct questions, I doubt you have continuing epididymitis; I cannot comment on your oral herpes; and I doubt you have genital herpes. You can be tested for HSV-2, the more common cause of genital herpes--but from your description, I doubt that's a problem. And of course a hundred things can cause stress and fatigue; I can't even guess about the possible causes. The other questions--about transmission of herpes, infertility, etc--would require me two write several pages. There are plenty of online sources for accurate information about genital herpes. Try the CDC (www.cdc.gov/std), the American Social Health Association (www.ashastd.org), and/or my former health department (www.metrokc.gov/health/apu/std).
Good luck-- HHH, MD