The primary use of the 5.4L is in the F-series pickup and E-series vans from 96 to present. The lightning, as you mentioned, has the supercharger.
There was a 4 valve version in the 2000 cobra R, but good luck finding one of those (only 300 made)
There is also a 4 valve version in the lincoln navigator I believe. It will never fit in a GT with the height of the intake manifold however. I think the lincoln is the only 5.4L with an aluminum block.
The 2004 F-150 has the new 3-valve 5.4L, complete with variable cam phasing.
In tuth, the 4.6L offers far more options. It came in 2-valve version in the continental, mustang, f-series, and many others from 93 to present.
4-valve versions came first in the lincoln MK-VIII and then in the 96-present Cobra. The 03 Cobra is of course supercharged. The 05 mustang GT will have a new 3-valve 4.6L with variable cam phasing.
In any event, these guys can get you just about any note worthy variant of the engine
http://www.karkraft.com/engines.htm
Also, if you are looking to build something with a little more power:
http://www.seanhylandmotorsport.com/
Sean Hyland can build about anything.
Good luck shoving a 5.4L, especially 4-valve, into a GT. It is wider than a 427 Cammer. Attached is the picture showing the difference between the 5.0L and 4.6L 4-valve. The 5.4L is even wider and taller.
Adam