Capt Al,
I didn't want to hijack your other thread regarding kit differences in case someone actually had some input on the subject (I'd love for FFR to jump in and spill some beans!)
Here's my take on the differences in the powertrains:
302/351 Pros:
Tried and true. Lots of options for aftermarket performance in every category. You can put 500+ HP on the stock internals. Has a more period correct look when topped off with a carb. The donor stock T-5 tranny will take a lot more HP than people give it credit if treated reasonably well. The EEC-IV doesn't have a lot of emissions programming to cause problems with aftermarket parts.
302/351 Cons:
You have to change just about everything above the shortblock from a 302 donor motor and add a supercharger to get 500+ HP. (Or you could go stroker motor in place of supercharging.) Donors are almost always high mileage requiring a rebuild.
4.6/5.4 DOHC Pros:
Forged crank from the factory. 6 bolt mains. Aluminum block in the 4.6 variety. Heads you'll never need to replace to get more power. A more unique look and IMO cleaner appearance than the 302EFI. Lower mileage donors with cleaner parts. Just a supercharger away from 500+ HP
4.6/5/4 DOHC Cons:
Stock rods aren't quite as good as the stock Windsor. More expensive donors. T-45 tranny not quite as strong as the T-5. EEC-V has more emissions code but it can be defeated with a chip. Not as many aftermarket vendors and parts are still pricey. Luckily you don't need a lot of them to make a lot of power.
Several of my friends race the mod motors with turbos (1300+ HP) or superchargers (1000+ HP) using stock heads and cranks! Here's an example of what you can do with a stock block, ported stock heads, and a stock crank (click on the image for a little video):
http://www.athenasofttech.com/images/cobra/host/EPSN0081.avi><IMG
This car and engine were built by one of my friends, Randy Haywood, who also drove the car in NMRA Super Street Outlaw to 7.99@175. He did use the 5.4 DOHC from the Lincoln Navigator, but the 4.6 DOHC can get close to this kind of performance with the same stock block, crank, and heads.
Note that I left out the 4.6 SOHC engines. They have better power in the later years, but they just don't have as much potential as the DOHC. I don't see the point in using one when you can grab a DOHC from the junkyard instead.
For me it was just something different to do. I've had a 302 with bunches of mods (Vortech S-trim, heads, cam, intake, TB, MAF, injectors) making around 500HP. I've had a 351W stroker motor (403CI) with a carb making around 700HP naturally aspirated. But several friends have very tame and streetable 500+ Mod motors so I thought I would try one.
Another possible plus for for the 4.6 kit from FFR will be that the position for the Cobra spec T-45 tranny crossmember is very close to where it needs to be for those who want a T-56. If FFR didn't account for this in the redesign I'm going to be a bit disappointed...