I think it would physically fit since the GT500 has the 5.4 in it. Can I ask why though? I am assuming you blew up the 4.6 and have a free 5.4? It is probably more work than it is worth. ModularFords is a good forum for the details on engine swaps like that.
Yes it will fit and your PCM will run BUT, not worth it even if you consider the small stuff like new lower manifold for your blower and intake air intake and weight.