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dth656, I ride a lot of both road and off road and knee pain is usually due to poor fit or a change in setup. I'd venture to guess that your change in pedals and cleats probably moved the cleat away from the ball of your foot, and that combined with less float works against you. If the soles of your new shoes are a different thickness than the old ones, and if the spindle height on the new pedals is different, it's possible that you're overextending your knee.
A proper fit is priceless, road or mountain, and a good fitter will be able to adjust things for your needs. It's best to take as much of your own stuff as possible; saddle, shoes, pedals, riding shorts, gloves, and if possible, bar and grips.
The distance from the top of your saddle to the spindle of the pedal should be the same for all riding, on all bikes. Some folks will lower the saddle position a centimeter or a little more for a cyclocross or downhill bike, but big adjustments from the ideal position are generally bad. The horizontal relationship between the saddle and the bottom bracket should also be constant for each bike, and specific to your fit.
Knee pain is bad, and should be addressed before it gets worse. A good fit should address this issue and provide a good dose of happiness.
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