Ernie,
I think there is even a 3rd version of the 5.4 motor.
Our Aussie Falcons get 2 different 5.4 motors as an option. The first is the same as the truck 5.4 I believe with 3 valve heads. The second is a motor developed by Ford Australia and is a 5.4 with the twin cam 4 valve Cobra R heads. These are installed in the XR8 Falcons and make 260KW (350HP) in base form and 290KW (390HP) in FPV (Ford Performance Vehicles) Trim.
I think this motor has a lot of potential for making good power. The only problem is the size of the thing, It's Huge!!! Ford had to put a huge hood bulge on the XR8 falcons to clear the intake manifold (it actually looks pretty cool). The motor is also very wide, much wider than the regular 5.4 because of the Cobra R heads. The deck height on the 5.4 is greater than the 4.6 Cobra R motor so it realy fills up the engine bay and there isn't much room left around the shock towers. The Falcon front suspension design incorperates a removable cross member because the engine has to be installed from underneath.
I don't think the XR8 5.4 will fit in a Cobra. If you did manage to get one in you would have to narrow the foot boxes so much you wouldn't have room for 3 pedals.
Check out some of the specs on the Aussie 5.4s here
Ford Performace Vehicles
Cheers