Bike store down the street from me said they would change cleat position for free and see if that helps. They said since I have flat feet (collapsed arch) I would need arch support, and need something cycling specific. Of course it's $90 in their store for their insole. I was thinking of just trying a dr scholls insert I have lying around or just a metatarsel gel insert. But maybe adjusting cleat position would put pressure farther back.
It's just odd that this is the first time this has happened. I have Shimano R133 shoes and Shimano 105 pedals. Perhaps riding MORE could alleviate the problem as I get used to putting pressure on this part of my feet.