Paul,
Here's one more shop that does the engine ==>
http://www.vtengines.com/
BTW you might also want to check out Metco Products ==>
http://www.metcomotorsports.com/ they are putting an engine from a GT500 into a FF Cobra.
Be sure to look at Sergio's website ==>>
www.cobra4m3.com he did one of the first modular motor installs and has quite a bit of good information available there.
For what it's worth a 4.6 barely fits into the car. A 5.4 will fit but you end up with substantially less than an inch of hood clearance. Normal engine rocking will hit the hood unless you solid mount the motor.
Ed