Might want to go see a Doc, could be Neuropathy related (especially if you have high arches).
+A million on a good, properly fitted shoe, along with some custom orthodics (although those can get expensive).
Personally I gave up running two years ago because foot pain. Switched over to an elliptical and honestly couldn't be happier, although I look like a complete fag whilst on one, and I miss the fresh air while running.