This was posted by someone earlier-
http://www.cptips.com/knee.htm
I've found it very interesting and am currently looking for pedals with more float for my knees. I'm also concentrating on spinning circles instead of mashing to save what I've got left.

I am NOT by any means an expert, nor do I play one on tv, but knee pain with the addition of clipless pedals means a need to adjust things. Cleat position, float, something.