I converted a 65 Mustang coupe to a 2004 4.6L SOHC. I converted the transmission too but kept the 8" rear end and added 3:73 gears, disc brakes and limited slip (conversion about $1500).
The shock towers had to go so I converted to a Heidt's rack and pinion disc brake front end (about $3500). I started with a 2004 engine from an explorer ($1500) and bought a police special 4R70W transmission ($800). I received the original computer with the engine but I used an after market wiring system which also updated the rest of the car wiring (about $4000 all done).
In order for the engine to fit in the engine compartment I cut the pan for the cross member.
I did this two years ago and there wasn't much available for help. It was hard but the outcome is great. I used a "chip" (several types available) and had it programmed for pump premium. I get 300 rear wheel HP and 21 MPG. The steering and brake upgrades make much difference in driving too.
I kept notes if you're interested.
By all means, take the time and do the conversion. It will be a challenge but worth it. here's a car that was done before mine and with probably much greater cost.
Year One Sourced 1969 Ford Mustang Parts - Hot Rod Magazine