I suspect the antibiotics you got initially were ceftriaxone (the shot) plus azithromycin (the 4 pills) which is highly effective treatment for gonorrhea. There have not been proven treatment failures to this regimen here in the U.S. I do not know why your doctor gave you the ciprofloxacin on top of your initial medications. This (ceftriaxone plus azithromycin) is the optimal treatment for gonorrhea, worldwide.
If you have been seen by a trained clinician who felt there was no indication for further treatment, I would defer to him. He had the chance to examine you and I have not. Your residual symptoms may be residual inflammation from your gonorrhea. Alternatively, sometimes after an exposure that, in retrospect, one wishes they had not had, persons tend to examine themselves and be far more attuned to genital sensations than in periods when they are not concerned.
Chronic gonorrhea used to cause sterility in men before the age of modern antibiotics. This no longer occurs. I would not worry.
Finally, I would follow the STD Clinic clinicians' advise, not go "doctor shopping". If you do go see other doctors, I suspect that sooner or later you will find one who will "treat" you with something as that is easier than telling you to wait. Unless there is objective evidence of infection however, it would not be the right thing to do or in your best interest.
Hope this helps. EWH
Dear Dr. Hook ,thank you for your advise it really helped me a lot with my anxiety, and I did not go "doctor shopping". I was indeed originally prescribed the medications that you deduced above. Today, on the 11th day since I got the initial treatment I noticed a sudden increase in the amount of discharge that I’ve been getting. So I contacted the same clinician. He was a little puzzled, took the small sample and said that he could not see any gonorrhea visually and that the discharge that is there "probably has to do with inflammation". He drew an analogy of physical impact that causes swelling and white blood cells in the area. However, he said that I still should not have sex until the discharge completely stops. Also, "just in case there is something" he prescribed me 4*100mg pills of metronidazole at once and 100mg doxycycline twice daily for 10 more days. He said that the urine DNA test for gonorrhea will probably give false positive at this point since there are probably still some dead bacteria there and that if symptoms continue after 10 days I should do that DNA test. I hope that it will work...
Thank you again.