It sounds like you've had a thorough work up so far to cover the bases for the usual suspects. Continuing to follow up with the urologist is the best course of action.http://www.pelvicpainhelp.com/
is a website I've always found incredibly interesting and I recommend it often. Might be some interesting reading while you are waiting for your follow up appointment. Lots of reading on the site without having to order their book.
Is this a std related issue? Not really. Normal mouth flora sometimes isn't so normal when it's introduced into the urethra thru oral sex but you've had countless urine samples given and many exams so any bacterial or funguses that you would've picked up then would've been detected for treatment by now. Even any viral causes would've run their course by now.
I'm sure this is incredibly frustrating for you though not to mention painful. I hope you get answers and relief soon for it all.