The urethral/penile symptoms you describe are atypical, but could have reflected urethritis (gonorrhea, chlamydia) or possibly--the 'gray patches'--herpes or syphilis. However, since all those tests were negative and after the treatment you have had (especially doxycycline), you can disregard those possibilities.
As to the foot/leg symptoms, no STD causes those, and neither does HIV. Whatever is going on almost certainly is just a coincidence with your sexual exposure. I suggest you follow your urologist's and or other providers' advice both about further diagnosis and treatment, but you can be certain you have nothing that will harm you or a future sex partner. Symptoms alone do not necessarily indicate disease.
Good luck-- HHH, MD
Thank you for your reassurance but I do have a few more questions-
1- Should I redo any of the tests or are these results reliable enough with respect to the time frame (30 days after exposure)?
2- As for Herpeselect I tested with Tstd and their website said the following about it