Knee Issue Finally Solved?

Besides the hassle of my recent broken collarbone, I've been haunted by a mysterious knee ache for about 2 months now and I'm pretty sure I have discovered what is causing the ache. I noticed while riding my new bike that during the crank rotation I feel a little "clunk" coming from the bike that resonates through the crank arm. I had Alex confirm what I was feeling last night. So in a typical 2.5 hour ride I figure my knee feels that little "clunk" about 12,000 times. :-(

Dang, I have cut my weeks down to just 200 miles due to the knee issue. I'll never get all those miles back. :-(