Old, old thread, but the solution for me, which is not mentioned here, custom orthotics. I originally got orthotics because of pain in the metatarsals on the outside of my foot. Without my orthotics I start getting unbearable hot foot after about 60 miles, and have to alter my pedal stroke to push down less and pull up more. With orthotics I've done rides over 500 miles with no significant foot problems.