New Pedals and cleats

[soprano]

Also consider the possibility that the stack height of your cycling shoes and pedals is different from what you had with the flat pedals and whatever shoes you wear with them. You may need to raise or lower your seatpost as well.

I second this. When I've changed pedals, I've always had to change my saddle height. It's amazing how a small difference in saddle height can just kill your knees.