Transmission Swap (Detailed Question)

[2001GTPEWTER]

I'm down to the engine and tranny now, I've got a few options but before I spent too much money I wanted to run a few things by anyone whos' installed transmissions on late model Mustangs.
The car has a 5-speed manual, I know putting in a 5-speed AOD would be more than just bolt and go, what exactly would I have to replace or remove to make that work?....Also, I'm not sure (since the 2003 Mach 1 was made in small numbers with an AOD) if the Ford 2003 AOD transmission will bolt with the engine, even if it originally came in a car with a 5-speed Manual.
Finally, is it possible for me to introduce the new engine computer with the instument cluster myself?..A friend of mine said I might be able to do it with a Predator tuner, but I think that was garbage.