Mine has the basic 03 Cobra engine except for the blower, block and fuel system. I swapped out the Eaton for a Whipple and used an aftermarket Aluminum block from Sean Hyland. The fuel system uses dual Ford GT pumps and 60# Mototrons with a custom fuel curve.
With the as delivered top pulley from Whipple and a stock lower pulley you engine will produce somewhere north of 600 FWHP and instantaneous maximum torque from about 2000 rpm to redline. BTW instantaneous maximum torque will be 550 lbs-ft sometimes a little more.
The 5.4 will probably not fit the engine bay. The 4.6 already uses up essentially the entire bay.
See Sergio's modular site =>
http://cobra4me.com/ for more info on the modular engine alternative.
Ed