I had the same issue that would pop up on rides over 50 miles. moving the cleats around, inserts and different pedals did not work. I have a hard time finding shoes that fit. I got a pair of mountain bike shoes that cost a bit of $ because they fit. No pain riding my mountain bike. These shoes had carbon soles. Changed the pedals on my road bike so I could us the mountain bike shoes and the pain went away. It had to do with the carbon sole, it is stiffer and prevented the point loads. Two years later I spent some $ on some nice Sidi road shoes with carbon soles and there is no pain. The less expensive shoes just dont don't seem to have the stiff sole and give me the foot pain.