Sometimes it doesn't matter about the size of the shoes, what kind of pedals are you using? If you are pushing down on a small pedal, then you need to get some sort of foot insert, or maybe a stiffer sole in your shoe, or even a pedal with a larger platform. It's pretty common and a lot of us fight it. I use Specialized foot inserts because they have the metatarsal buttons which spread the nerves and bones (or something like that) back out. I tend to have it on one side only too. I did have a back injury a long time ago, with pain down my left leg. I thought that was it, but lately I notice that if I coast, my left foot is the one that is down. Maybe that's part of it too. Do a search on hot foot and you'll find all kinds of information.