Good for you Foo2. When I first read the thread I thought it was going to be about watching a marathon from your couch.
Chondromalacia Patella. Bummer. I have the same thing from years of skiing. It sometimes feels like somebody is stabbing me with an ice-pick right in the center of my knee cap. Does that sound about right?
A couple of things have helped me tremendously.
1) Strengthen the calf and quad muscles uniformly.
2) Avoid running on hard surfaces. Run on grass or a soft track.
3) Proper shoes.
Take This Simple Test To Learn Your Foot Type
Check out this link to see what shoes might be good for you. The proper shoes made a huge difference.