I guess it depends on how you're defining "shell", to me a shell is only the body, possibly the dashboard...no axles, seat, fuel tank, etc. That seems to me to be more expensive versus buying a wrecked GT and a decent V6 body and swapping the goods over to the GT. Heck, you could probably find a high-mileage manual GT for cheap and invest is a low mileage engine and rebuilt transmission.
The bodies are all the same, just different things like front and rear bumpers, foglights, wheels, side scoops, hood, spoiler, and the Mach I has a different panel over the rear side windows (now would be a good time to figure out how you want your car to look, so you don't waste money buying what you don't need). The computer system and wiring are gonna be the biggest pain.
Swapping from a auto to manual is probably more expensive than investing in a manual in the first place (unless your two cars are good enough to use as a donor). The biggest problem with a auto-to-manual swap is gonna be the computer/wiring. You may be able to reuse the autos radiator, but I'm not too confident about that.
Sadie- '04 GT Auto- RMR#4837, 4-Point-SEXY