Clearly you have no STD, and that's all that I deal with. However, the combination of possible arthritis (knee swelling) and an 'itchy spot' on your penis suggests a possibility of reactive arthritis, formerly called Reiter's syndrome. RA sometimes is an immunologic reaction to a chlamydial infection or to any of several non-STD problems, especially intestinal infections.
I doubt RA explains your problems, but you might raise the idea with your doc just to be safe, or ask for referral to an arthritis specialist. However, if that's what it is, it probably never will seriously harm your health, and it is not communicable. Given the treatments you have had, you can be 100% certain you don't have any STD or other infection that will ever seriously harm your health (except perhaps your mental health) or that of your wife or other sex partner(s).
Otherwise I can't help. I don't deal with health problems other than STD on this forum.
Good luck-- HHH, MD
HHH, MD