For what it's worth, I was having the same problems right after I switched to clipless pedals/shoes. At first it was because I was strapping the shoes on too tightly. That helped the immediate (15-30 minutes) onslaught of toe numbness, but it still came on after about an hour. So I moved the cleats back and this weekend did an (at least) 3 hour ride with no numbness whatsoever.
Tim.