I had a lot of foot discomfort- numb toes, hot foot, cramping- when I recently switched from mountain biking pedals/shoes to road shoes and speedplay Xs. Turns out my road shoes were too narrow.

I switched to new shoes with a moldable insole (shimanos), and am very careful not to strap them too tightly. This has completely solved the foot problem.

Other tips: tight socks can contribute to this problem, in my experience. Also, my feet swell during the course of a long hot ride, so I sometimes loosen shoe straps mid-ride.

Try really loosening your shoes when the problem starts on a ride. If loosening the straps (a lot) helps with the discomfort, your shoes are probably too narrow/tight.