Quick question for you 4.6 guys.

Nope. You would have to swap the whole intake manifold, and I dont see that working out coming from a 4v to a 2v 4.6.

The GT has a little plenum sitting ontop of the lower intake manifold.

The Cobra has a more traditional styled intake manifold, no small plenum.
 
the dohc 4.6 does not have a removable plenum like the 2v does... are you talking about the throttle body? even that won't fit, its a dual-bore (twin 57mm i think) setup, and will definitely not work on your car. Short answer - no, 4V parts can not be used on a 2V motor