Did they do an actual prostate exam using fingers or an MRI to look at your prostate and scrotum?
If they haven't, that's what I'd suggest.
Everything you are saying suggests prostatitis. You can have non-bacterial prostatitis, and an x-ray doesn't always show inflammation of the prostate.
Everything about your symptoms screams prostatitis to me. I am not a doctor, and can not diagnose. I'd get a second opinion from another urologist.
Let us know what happens.