I used to have foot issues as well. It got to the point where I have a "protrusion", sort of a calcium build up if I understood my doctor correctly, on my left foot. In any case I changed several things which have solved my problem. I bought a pair of stiff road shoes with a wide base road pedal. This prevent the shoe from flexing and digging/rubbing into my feet. The second component and equally helpful, is that I try to spin more than before. This really helps with the amount of pressure I put on my feet during rides.

in your case, what kind of shoes are you wearing? Do they flex while you are pedaling (so it feels like you are only pushing down on your cleat)? If so, you may want some stiff road shoes. Hope it helps.