hey bro,
sorry to hear about your condition, sounds like your doc has his head buried up his butt,, if its been 2 years i have to ask, have you or did you see a physical therapist? if not i would highly recommend you doing so, since the first step in getting your knee back to health is by the proper exercises that a physical therapist can help you out with, that and rest , but if its been 2 years i would suggest finding a new doctor that will properly treat your problem, would hate to give you any exercise advice with out you first having your knee checked out with a professional, like i said, find a new doctor and see if he cant recheck the knee or recommend you to a specialist,
good link if you have not already read it about runners knee
Chondromalacia - Runners Knee - Chondromalacia Treatment