Chiming in a little late, but I did C25K and have a bum knee.
I first dislocated it over 20 years ago but since then it has popped out at least 5 times. The first time, of course, was the worst as it popped out and had to be popped back in--ahhh, fun times.
I've never had surgery, but back in H.S. I ran exactly one CC race, got injured and was told by the athletic trainer at school that I 'should not continue running because my knee cap could pop out at anytime'--
. Granted, he's wasn't a dr, but it was enough to scare me.
Needless to say, I quit running CC at that time.
Fast forward 20+ years, 4 kids and a good 70 lbs later my knee was beyond shot. So once I started exercising back in April I made sure to take it easy on it--no running at all. I did, however, start strength training. I honestly think that made all the difference in the world with my knees. I didn't have any problems with my knees for most of the C25K program. I did start experiencing some pain about 2 weeks into running the full 3 miles, but I bought a brace and wearing that has eliminated nearly all the discomfort.
My knee isn't as bad off as yours sounds--Never had surgery or anything, but perhaps strengthening the muscles of your knee would help to keep things where they're supposed to be? And of course, wearing some sort of brace. Whatever you do, just take it easy and if you find yourself in pain--stop. There's no sense in blowing out your knee again.
Hope you can start running again, it sounds like you're really itchin' to run!