Pain in the outside of the knee sounds like ITB trouble to me.... get a foam roller and stretch it out regularly; westtexas posted some exercises in the Health section.

Now to the subject of pedals: Personally, I felt my ITB tensing up when I swapped my cleats for some that allowed more float (I use Look pedals and installed red cleat, with 9 degrees of float, having used the gray ones, with 4.5 degrees of float before.. I did notice that when my ITB was unhappy, I was toeing-in in the pedals. I make a conscious effort not to do that.