Could be your shoes are too tight or too small. I discovered that I ride with my feet rolled outward..go figure and bought wider BMX style pedals. To my surprise, they worked! More leverage and power as well. I can't ride clipless w/o killing myself despite having an awesome pair of shoes that fit perfectly. I bought cheapie 15 dollar BMX style pedals, but they make nicer ones with and w/o clips. I do more mountain biking than road, but plan on putting wider pedals on my Fargo.
Despite the pedals, when I saw my podiatrist a couple of weeks ago about pain in the balls of my feet, he said my soft tissues had swollen up around the nerves causing major irritation. If your are dealing with numbness and pain for a couple of hours afterwards, you're putting pressure on your nerves. Make sure your shoes are properly fitted and the pedals set up for how you pedal. I'm on an anti-immflamatory right now.