I'll throw out bike fit as a non issue and take another guess... i'd put dollars to donuts that it's about form more than anything else.
do you have a smooth spin? try pedaling with one foot and you'll find out real quick how smooth your spin is.
do you stand out of the saddle at least once an hour?
do you have too much weight on your hands? this usually happens when you let your core muscles go slack.
do you have high cadence spinning in your bag of tricks? it's not necessary to always spin a high cadence, but it will take the pressure off the feet.