Welcome to the Forum.  Interpretation of STI tests taken when a person is taking antibiotics can be challenging.  Could you tell me what antibiotics you were taking at the time you were tested and for what?  Not all antibiotics work for all STIs.

Your symptoms- discomfort on urination, redness, and discharge from your penis are all signs of a possible STI.  To sort this out, I would suggest that you see a health care provider and seek testing for the most common STIs- gonorrhea, chlamydia, and perhaps Mycoplasma genitalium and have a urinalysis performed on a urine collection collected as you begin to urinate (the STI tests can be done on the same voided urine specimen).  This information, combined with examination by a trained clinician will help you to sort things out.   I would urge you to seek testing and not allow your clinician to simply give you antibiotics without knowing what it is you are trying to treat- that you have had this for over six months means it is not emergent and you will be better off knowing what is being treated than guessing.  If you have a regular sex partner you may also wish to have them checked as well.  Sometimes infections present in one partner are more easily detected in the other.

I hope these suggestions are helpful.  If you have further questions or, once you have gotten tested, you would like further comment, please feel free to use your up to two follow-up questions for clarification.  EWH

If you have taken those medications for more than a week continuously, the likelihood of most bacterial STI is close to zero.  Trichamonas and M. genitalium remain possibilities which might be tested for.  The sores on your palate are similarly not suggestive of any STI, including HSV (Herpes typically occurs on the lips and soft tissue).  Further your HIV tests are definitive and nothing you describe suggests HIV.

So, what to do:

1.  consider testing for M. genitalium and trichamonas using a urine specimen as suggested above.  I doubt that either of these is present but I think the testing will give you peace of mind. 

2.  Consider other non-STI possibilities, discussing your symptoms with not only your family doctor but also possibly a rheumatologist or a urologist (I will leave this up to you and your primary care provider, it is beyond the scope of this forum).

Hope this helps.  EWH

Cipro would have no effect on trichamonas and there is some resistance to fluroquinone antibiotics (including Cipro) in Mycoplasma genitalium.  As I told you, I am quite skeptical that your symptoms are due to an STI or related to the exposure you have described and think you should probably be looking elsewhere for the cause of your symptoms.

This is my 3rd response to questions as part of this thread.  Thus, as per Forum guidelines, this thread will be closed later today.  EWH