If you're racing I'm assuming your bike's pretty damn well fitted to you.
However, your new pedals might have thrown off your riding form just enough to make your knees go bad. Unlikely, yes, but could be a cause. This is something to fix back up when you're back up and riding again.
For the time being, take it easy and do some swimming. Swimming and cycling are pretty much the lowest-impact excersices you can do for your body. Stop immediately if the pain comes back, though.