i don't know if i am missing something here, but you have not sat on your bike for 2-1/2 months, you've consulted your physician, had x-rays and c-scans with no results - now you are doing physical therapy with your PT also puzzled but will just work on it - and recently you are looking on an internet forum for a secret stretch that will magically heal your constantly inflammed knee;

i will say it again, look for and consult a Sports Medicine Physician - bonus if the physician has experience with Cyclists - perhaps contact local Cycling Clubs/ Racing Teams to see if they can recomment anyone.

don't get me wrong, a lot of the hints here are good, and seem like good maintenance/preventive exercises for minor knee pain...i think you are well beyond that point