I've been commuting now to work for the last 2 weeks on my new clipless pedals (Crank Bros Candy pedals + Specialized Tahoe shoes). I've noticed, since Day 1, when I get about 2 miles into my commute, the ball of my left foot gets a bad hotspot that doesn't go away, and the outside of my left knee hurts. I've raised my seat so that I don't have much of a bend in my knee, but the higher seat height has not solved the issue. Any suggestions?