I hope all is alright, even though I do not know you (I'm new). I've had similar cases happen to me, but not as extreme... I'm sure the doctors have told you this by now, but you probably should avoid major exercising that puts strain on your knees. Just lightly stretch your legs when they hurt and take it easy, you know? If you go to the gym, don't use the bicycle or even the treadmill - go for a less pressuring equipment such as the elliptical machine.
I hope you're doing well and there is no real harsh damage...