Pain behind the kneecap is probably not chondromalacia. Not after 47 miles on a 30 year old...

By you saying your feet point out alot when you walk, you could have flat feet or excessive angulation in your foot, ankle, tibia/fibula, knee or hip. Without examining you I can't really tell.

I would try to find a sports-medicine oriented doctor and talk to him/her about your knee pain. You might want to go back to your toeclips for now. You don't want to do permanent damage to your patellofemoral joint or cause your patella to permanently track incorrectly.

*Standard disclaimer: Talk to your own doctor about your own specific problems. While I'm someone's doctor, I'm not yours.