Not just the shoes and saddle
I have this same problem, even happens when I have to keep my foot down on the clutch of the car for any lengthy period of time. Pressure on the foot in that region for long periods causes my foot to go numb. Both feet do it when cycling, and I do the toe wiggling thing and it eleviates it slightly. Must have arteries that run that area or something that don't like the pressure.
Also, it may be that your seat is too high that your having to reach and pointing toe down more then heel down during your down strokes.
Possible that your saddle is cutting your circulation off somewhere down the back of thighs. It's crazy isn't it...the numerous factors for each persons individual issues.