I have long feet and at first tended to set my foot too far forward on the pedal. This was to avoid fouling the chain stays or even the rear-wheel quick-release lever with my heels. Setting my shoes to put the ball of the foot over the pedal spindle moved the foot back a bit which, counter-intuitively, solved the chain-stay problem. The quick release lever problem was solved by closing it to the rear. With the foot too far forward, I also suffered aching arches on occasion but with the foot correctly placed the problem was largely solved.