Switching to Speed Plays and getting some float on my pedals... and getting a computer with cadence and keeping my cadence between 90-100 fixed my accute knee pain.
It took about 2 months of slow riding to get past it... after the damage was done... but those two things mentioned above are what did it. No knee pain since there.
Good luck!
"Life is not a journey to the grave with the intention of arriving safely in a pretty and well preserved body, but rather, to skid in broadside thoroughly used-up, totally worn out, and loudly proclaiming: WOW WHAT A RIDE!!!!"