Many thanks for your answer and my apologies for not being clear in my description of the problem. I was never prescribed any medication since the urine tests came out clear and the doctor advised me to just take lots of fluids. Without any medication I happened to have come back to normal meaning that the urgency to urinate very frequently went away on its own and that the burning discomfort also subsided itself. This sensation though did not go away completely as after every 6 days of complete calm i.e. no such sensation at all I get this sensation all over again for a day or two max. I may need to consult a urologist but through your opinion wanted to rule out STD's at least.
There may be something missing from your post. I do not see what infections you are concerned about and did not see that you were treated for gonorrhea and chlamydia until I got to your questions. I doubt that this makes much of a difference in my answers however. Before I get to your specific questions, I have to say that there is not much in what I have read to suggest that you have an STD. You used a condom and if you used it correctly, even if your partner was infected, you would have been well protected. This conclusion is further supported by the negative tests you , including the complete absence of inflammation on your urinalysis. Finally, it sounds as though, despite any clear indication, you have been treated for gonorrhea and chlamydia infection,. This therapy would have also cured NGU, eliminating any and all casual agents which might have been concerned about. Now, on to your questions:
1. Yes. Tests for gonorrhea and chlamydia are typically positive after 2-3 days. 10 days is certainly enough.
2. Typically the urine tests should be sufficient. In addition, having now apparently been treated, any abnormality detected at this time would suggest a problem other than STD.
3. Strange urethral sensations are notoriously difficult to sort out and far more often than not, turn out to be non-specific and not associated with infection or other abnormality. Not sure if it pertains in your situation or not but anxiety can do this.
Hope these comments help. EWH