What pedals and shoes did you get?
If you have clipless pedals, your foot is now pretty much locked into place, with only a small degree of "travel" available. This means that you're no longer able to move your foot around as much, so every pedal stroke is pretty much the same. Therefore, there's more potential for repetitive motion injuries. This means that it's pretty important to have the right pedals for your knees, and your cleats adjusted properly.
You might consider having a fitter adjust your cleats for you. It is possible to do it yourself, but that's not something I have experience in.