Hey John~
welcome to kneegeeks. i hope that u find the answers that you need here, this site has been such a help to many.
anyways, im sorry to hear of the knee pain. if u have had this pain for as long as you have with no relief from the PT, then i strongly suggest that you get it looked at by another OS. the clicking that you describe can be a number of things thats why u should get it looked at. my clicking that i had before my surgery was due to my knees being malaligned and i also had patello femoral pain (PFS).
until you get into the OS, just rest take it easy and ice alot. if you need any pain relief you may wanna try OTC stuff like Motrin, Tylenol, or advil. i hope this has helped you at least a little.
good luck
~Mandy