The moment you have all been waiting for:
It seems like my measurements were correct and I did fall about 2 inches short of the template but the little gain I might achieve by correcting this would not be worth my time. the edges are very round so hopefully I'll get an "EV1 effect" that allows the side flow to make up for the high top angle. The hatch has always had a little movement, so I'm going to be using some rubber stoppers to keep it in place. This should lift the hatch up about 1/4" which when translated over 4 feet might lift me up closer to the template. I can shake the whole car from the tail. Except for the slight movement of the hatch itself, this thing is solid.
Here's the original shot before I used the template tool:
The hatch will be completely operable except you will have to open it using the button from the interior. I may devise some sort of "key-on-a-pole inside the tail, but I need to avoid someone punching through the coroplast and opening my car up.
For a rear window, I plan to use one big piece for the top of the tail.
I eventually plan to get a rear view camera and replace my side view mirrors with cameras, so blind spots wont be much of a concern but I'll have the large window as a back up. I'll just need to be cautious when changing lanes.
As far as color goes, I planned on using Krylon Fusion Gloss Hunter Green. If you think black would look better I might have to go that route. I was also thinking of using a rough "bedliner" type coating to hide things.