Yeah, that is probably it, I heard some cyclists need to shim one side of their foot while riding because when they walk they put more weight on the outside of their foot, like the right side on their right foot. With clip-less shoes(or any shoes) this is fixed with shimmed soles. I want to shim the outside of the peddle, when I walk I walk on more of the outside of my foot. After the guy who fit my bike told me that I searched and sure enough that is probably the problem.
The problem with using a custom insole is I can't really use them with keen sandals, my preferred footwear in warm conditions. If I need to I'll go that rout, getting a different shoe, but if the toe clip on the front of my peddle holds my foot in the same position couldn't I shim my peddle and achieve the same affect?
The pedals I have right now have 'fixed' nubs to keep my foot from sliding around the pedals, not the ones that have the replaceable bolts. So I ordered some ones with replaceable bolts.
Basically it causes pain that lasts for a few nights, I have to elevate my right let when I sleep on my side because it is so sore.
That is what I think I have except I need to shim the opposite way I think. It doesn't cause knee pain, after the fit I don't experience knee pain at all, but my foot goes slightly to sleep and my upper leg, outside of leg close to the hip, gets sore. Or maybe I do need to shim this way, not sure. I'll have to email him and ask. He fits mainly for people that have clip-less shoes and that is a easy fix for those.