Donna,Yes, you are no doubt correct, that resurrected people won't need to be restricted to a 21% O2 atmosphere.So, that is a good point about the upper portion of the new Jerusalem.
The other thing that I had been wondering about, though, in the letter, was about the bottom of the new Jerusalem.The bottom of the new Jerusalem is apparently a square of about 1500 miles by 1500 miles.1500 miles is close to ⅕ of the diameter of the current earth.If the new Jerusalem has a flat, square bottom, and it was to sit upon the current earth, the gates would be close to 70 miles up, above the ground.So, if the new Jerusalem is a cube, as you pointed out, then this would be similar to a square block, 1.64 inches on each side, sitting upon a soccer ball.
That is why I was wondering if the new earth might be significantly larger than the current earth.This way, without the sea, there could be a portion of the surface, which could be level, like a plateau, where the new Jerusalem could sit upon.And the gates, would then be all at ground level.