The 4.6 dohc came in Mark VIIIs, '96-'04 Cobra, Aviator, and Continental (front wheel drive, won't fit rear wheel trany). The 5.4 dohc came in the Navigator and GT (GT40).
The aluminum block 4.6 dohc has 6-bolt mains.
They're swapping the 4.6 dohc engines into all sorts of vehicles. You can even get a swap kit to put one in a Focus! And it all bolts in, even the mustang 8.8" rear axle.
I dropped one into my '98 Ranger and it really wasn't all that difficult.