Diagrams look good, and a damn fine first post!
1) Think about moving your wiring closet to your mechanical room if there's space. May be easier to mount stuff on the walls, and get wiring in/out of that area instead of under the stairs.
2) Don't use in-ceiling speakers in your great room for L/C/R. Bring them down to at least in-wall height.
3) Surround locations don't look correct for 7.1 in the great room.
4) Also for the GR, use your surround speakers for whole-house audio (using a speaker interrupt/switch), or just take a line-level output from the WHA system to your surround receiver.
5) Master bedroom - think about moving the speakers to flank the head of the bed, then you can set up for a future surround receiver (same speaker interrupt concept as the Great Room), in addition to WHA.
6) Why a pocket door on the guest room?
7) With only 3 video zones, and DirecTV, you might just use individual receivers for all three, and the whole-house-DVR feature to share content. Much simpler/cheaper than distributing HDMI. (But yes, pre-wire to allow for it!) The computer could be a simple HDMI splitter/extender depending on where you want to use it.
8) From a pre-wire perspective, wire for video capability on the terrace and in the garage. "Rooftop party for sporting event"?