you cant use the trans unless, you get the tail shaft from a 2001-04 3650, and as far as the motor goes, it bolts in, with the stock 4.6 mounts, off a 96-04 car, and logan motorsports, makes a kit for your 2v headers and all to bolt on. you will need cam phaser lock-outs, for the vct. the rest will plug in and run. pretty simple.
What about hood clearance for the 3V intake? I've heard a stock hood won't clear the front of the intake/TB/inlet tube and that a cowl hood, or a cutout covered with a blister or scoop is needed.