Will also go on each side of garage door and at the bottom of the post at the left side of this picture (which may not show well).

Also any advice on how to fill the empty space above the entry door would be much appreciated (where there is no window but it looks like there should be for symmetry).

Since they are sliding doors won't there be steps or a deck in front of them? Who would see the stone?

I don't think anything is needed above the door but a close up picture of the entrance would help.

1- Do not stop the stone at the bottom of the doors, I'd say go about 2/3ft up the doorway height with a sill along the top.

2-Questions. What is going above the stone? Is the stone wrapping around the house or just being applied to the front facing walls? If it will be wrapped I think it'd look very nice and you don't necessarily have to take it through the porch space because the stone will be pulled in on the columns.

3- Is there going to be a deck in front of the house for the sliding doors?

4- No window needed above the door, it will not bring in much light so high up with a roof above it. Just add a nice pendant light there.