Penis pain at the tip & around perinium for 2 years. found klebsiellia in semen. bacteria now gone after treatment but pain remains. what is happening?

Chronic Prostatitis: Since this has been going on for so long it sounds like Chronic Prostatis/Chronic Pelvic Pain Syndrome. This is a diagnosis of exclusion and other causes should be ruled out, such as urethritis, UTI, Urethral Stricture, urogenital cancer.. I would suggest evaluation by a urologist if not already done. There are effective treatments availble for your pain.