Coyote wagon,
Welcome to the forum. Sounds like you have an awesome project underway.
I have no experience with swapping in a Coyote with auto into another car but I have read a few threads where lads have switched from manual to auto in their cars. I'll just give a 10,000 ft flyover reply becuase the swap is fairly technical and I don't remember all the details.
There are a lot of things that need to be tended to because they all speak to each other and one item one will not work unless the VIN info is consistent with the other items. Fortunately, your local Ford dealer (and some tuners) has the IDS instrument to look through the network and activate or deactivate stuff you won't have on the project car. If you want to do it yourself, you will have to find some techie threads on this forum and others where the enthusiast did a full swap from manual to auto transmission. I will see if I can find some helpful/informative links for you to peruse.
edit**
PM sent with links!
end of edit***
Chris