Do you "stretch" your foot before you ride? before every session I do a complete stretch but I also stretch my foot, lean foward against a wall put ur foot back as if you were stretching your calves but roll onto your toes so your heel is in the air and only the bottom of your toes are on the floor and you will feel your foot stretch, if I forget this stretch I get the pain also by mid day. try that.
Im just throwing this out there also but its not like something is digging into your foot right? if it is then you should check your bindings and make sure your "gas peddle" on the footbed is pulled out to where its supposed to be and not to far back under your foot.