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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?
I agree, also the way your toes may be pointing. Is there any play in the cleat? I keep my cleats super loose so I can slightly adjust my foot as I pedal.
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.
I would also suggest checking your cleat rotation. When you stand naturally, do you toe in or out on that side. It may not be even side to side and that's OK. The way I check clients when I do fittings is to get them to barefoot run on the spot for about 5 steps per foot, small steps, then stop suddenly and look at where they land. If you naturally toe in or out, your cleats should be adjusted to allow this natural foot position to occur.
Also, putting your cleats farther back on the shoe can decrease hot spots and the ball of the foot.
It does sound like whatever is going on is irritating your IT band complex so using a foam roller on your thigh and hip can be helpful as someone else has mentioned above. You want to focus on the outer and front thigh and hip, and the back of the hip.