I agree with your urologist in all respects. Your current symptoms do not suggest any STD and are unrelated to your sexual adventure over a year ago. Your girlfriend is not at risk of anything, and you have nothing that will ever harm you. (And I am skeptical about the epididymitis diagnosis.) Your later symptoms did not clear up with doxycycline because you have no infection, as your urologist apparently told you. You have male pelvic pain syndrome, which is often (usually? always?) a manifestation of genitally focussed anxiety, which in turn can result from an anxiety-producing sexual encounter.
Read this thread from a week ago:
http://www.medhelp.org/forums/STD/messages/4380.html
Also look at this link, which was posted in that thread: http://www.pelvicpainhelp.com/excerpts.html
Good luck-- HHH, MD