God luck friend. You are going to have a lot of trouble fitting that 4.6 block in your 5.0. You might have to cut your shock towers out and make a tubular sub frame, possibly use a heidts front end or something. The car just isn't big enough, that's why it hasn't been done yet.
if you can get the motor in, just put a matching
tranny on it. then get a custom driveshaft made to meet up with your existing rear end.
for the money you are going to sink into this project, you could by an '03 cobra or something.
but good luck! you're gonna need it!
and the 5.0 isn't primative. it's just a different motor. there is a reason the 302 is still around. the mod motor is a way for ford to cut down on manufacturing costs. wait till you see how much it costs to modify that 4.6

__________________
1965 Mustang Coupe Project: 1965 Mustang Inline 6 (For Now) Coupe, New Floors, New Quarters | Ford 9 Inch Rear, 11" Rear Disc Brakes, 3.50:1 Gears | Control Freak Front U/L Control Arms, Global West Adj. Strut Rods | KYB Gas-A-Justs, Grab-A-Trak 620 Coils & Mid-Eye 5-Leafs | Global West Tubular Subframe Connectors | Addco 1-1/8 Front Swaybar Kit