I agree, there is definitely a concern about an STD from this encounter. One thing that I am thinking might be a possibility is related to gonnorhea. I know that you were tested for this, but it might very well fit. It can become disseminated and go to other parts of the body, and there is a description of it causing a type of arthritis. If you were googling it, you would put in "disseminated gonococcal infection". Here are the test that might be done to diagnose this:
1. At least two sets of blood cultures should be obtained from all patients with suspected DGI. Cultures are diagnostic when positive, and are also helpful in separating DGI from other conditions.
2. Patients with the clinical features of DGI should have synovial, skin, urethral or cervical cultures, and rectal cultures submitted on Thayer-Martin media. Approximately 50 percent of patients with DGI have positive cultures from one of the last three mucosal sites. If associated urethritis (pain in the urethra) is simultaneously present, a Gram stain of the urethral exudate should be obtained and examined for the presence of the gram negative diplococci characteristic of N. gonorrhoeae infection.
So in other words, you need further evaluation. This might involve going back to RE-SWAB the urethra and LOOKING AT IT under a microscope to see if these bacteria are present. If there is significant joint involvement, there might even need to be sampling of fluid from a joint. My strongest recommendation is that you seek an opinion from an INFECTIOUS DISEASE specialist.
I hope this is a good start - please let me know if you have more questions and I will continue to help you through this!.