I feel for you. I have this problem also whenever I ride over 30 miles. It is a killer. In fact I dread that 30 mile mark... I use mtb shoes and clipless pedals. I've upgraded shoes with not a big improvement. Next is to try road shoes and pedals.

Also fool around with the cleat position. Best thing is to move it back toward your arch.

From what I undestand you are pinching the nerves that run between your toes.

Don't give up.
SKM