That swap sounds great! I did it with a 5.4 and you can see in my signature that I used a GT500 PCM and engine harness because I knew I wanted to run a GT500 blower in the future, so it was easier.
Honestly, you could run the 3V PCM and modify the harness. I think the guy is still on here with the dark blue Mustang that did it that way (pretty sure he shut off the passenger cam position sensor and all that 3V cam stuff in the tune). And as far as the wireless throttle, that is as easy as a homemade 1/2" adapter plate, no point trying to do the cable.
If you are using your 4.6 shortblock and just putting heads and the timing cover on it, no problem with motor mounts and mount "ears". MMR makes the plates for other blocks, I used the GT500 iron mount ears for my 5.4. I am sure that you know that your 3V has a 6-bolt flywheel and you probably want to go forged pistons/rods/crank for your turbo, so you need an 8-bolt flywheel (best to buy with your clutch as an SFI rated setup, like Ram dual-disc Force 9.5). Trans bolts right up and will work until it breaks from hp/tq increase.
If you are running a 99-01 Cobra or 03/04 Mach upper and lower intake manifold, you can keep your 3V alternator + Cobra bracket right where it is, but the t-body/air inlet is on the "crowded" side of the engine compartment. You could use the 03/04 Mercury Marauder upper (same lower as Cobra/Mach) to put the t-body on the driver's side. The 4.6 DOHC has the black steel pipe for the coolant crossover. The Air conditioning compressor remains as it is. The power steering pump is mounted the same place. You can put on the 13/14 GT500 cast oil pan for lots of volume. The Cobra iron exhaust manifolds fit without any issues (I even ran them on my wider 5.4 without any mods), but your turbo will change all of that to custom.
It's actually a really easy swap if you take out the complexity of your turbo piping/components. The best part is that all of your gauges and everything else will work (anti-Coyote pitch there)!
After all of that, it's all about the tuner.