the shoe feels fine when I just put it on, but after a little pedaling, I get a pain the starts towards the ball of my foot. Then it spreads to the rest of the bottom of my foot, are you sure it's got nothing to do with cleat placement?
I suspect that if you look on the shoe and pedal manufacturers' websites you will find information on how they recommend cleat placement to be done. That would be a good first step in figuring out whether you have things set up correctly (at least ballpark).
From there you could go to a local bike shop and see if they are willing/able to help you on your position. Let us know.