The treatments you have had definitely would have cured gonorrhea or chlamydia, and I do not have a good explanation for the pain you describe. However, it is normal for any injured body part to be painful from time to time (sometimes continuously) after the problem has healed by all standard measures. For example, a person who sprains an ankle may have residual pain months after the ankle has healed; or someone who had an ulcer may have ulcer-like abdominal pain long after the ulcer heals. The same is true of the genital tract and probably explains some cases of persisting pain, discomfort, or other irritative symptoms following various STDs. Many urologists and other specialists use the term "male pelvic pain syndrome"; sometimes it is due to prostate gland infection, but most often no infection can be found and antibiotic treatment doesn't help.
Most likely it will fade with time, but see your doctor if pain continues beyond a few weeks, or if other definite symptoms of infection appear (cloudy or yellowish penile discharge, burning on urination, fever, blood in urine, etc). Or if you're just in doubt and would like further reassurance. But in the meantime, it is unlikely there is anything serious going on either for your health or that of your current or future sex partners.
Good luck-- HHH, MD