I practice using the classical position + footrest. After an hour or two of practicing, my left thigh begins to have a mix of numbness and pain.

When I stand up, I also don't last for very long.. the part near my neck where the strap rests starts to hurt a lot.
I had the same thigh pain as you. It got really bad. I figured out it was the elevation from the foot stool. So what I did was keep both of my feed flat, and use a small pillow under the left guitar horn to hold it at the classical angle. Basically did the same thing as a foot stool, just more of a guitar stool. Hope that helps. You must get used to standing, not much to do there..
Quote by AeolianSeventh
Maybe there are gnomes in your air conditioning vents using out-of-phase parabolic speakers to deaden vibrations from a distance.
Hmmm it sounds like either you have really bad circulation, or your muscles just aren't used to the exertion. I would guess the latter.

Also, you might want to check that you're not putting the footstool too high, and it can help to make sure it slopes away from you, and not towards (this is how your foot naturally slopes, no?).