If you do a Coyote, you definitely need to stay with the Ford EFI and all the electronic controls. The Coyote owes most of its stellar performance to the powerful and advanced EFI system it has. For example, most guys are getting dyno numbers of 360+ at the tire with those cars in stock form. With little more than a tune, some guys are nearing 400. In the latest issue of Hot Rod, they have a feature car that is an old roadster pickup with the new Coyote in it. They wanted the engine to look retro, so they made custom cam covers and an intake for it. In the process, they disabled a lot of the original Ford engine controls, including the TiVVT. When they dynoed it afterwords, it made barely 300 to the tire.
Now, I'm sure with some tuning and tweaking, they'll probably make more (the article claims they'll make "100 more hp"), but the stock Ford setup seems pretty capable as-is.
Besides, I don't know if they're even making an aftermarket carb intake for the Coyote yet.