Have you tried using a knee support when exercising?
I've got loads of problems with my hips and knees due to flat feet, they're all twisted and warped, and i find that when my knees start to play up a nice fabric (the neoprene ones just get sweaty and nasty) support does wonders.
Beyond that, i can't really help beyond offering lots of good luck and wellwishing on the road to recovery!
