Something else to consider is your pedal stroke.
Many cyclists tend to do all their pedaling on the downstroke, instead of pedaling circles (push down, pull back, then pull up and over. ) All that continual downward pressure on the ball of your foot can make your toes go to sleep.
I suffer from toes falling asleep occasionally (happens more in my Sidis than my other shoes, no doubt due to the very thin, not-very-cushiony footbed). When this happens, I make a conscious effort to make nice round pedal strokes and this almost always brings the feeling back into my toes.
To practice this, and really get an idea for what pedaling circles feels like, unclip one foot and do all the pedaling with the other. You'll soon find the dead spot(s) in your pedal stroke. Do this a few times on both legs, then try to apply the same technique with both feet clipped in.
Now, if I could only get myself to more often practice what I preach, my toes would fall aspleep less often!
