In a nut shell. The f-150 4.6 1997-2000 are Non Pi heads. All the other years through 2004 heritage are Pi heads. I beleive 2006 saw the 3 valve for the 4.6.
5.4 97-98 non pi. 1999+ Pi heads. 2004 3 valve for the new model while the heritage still had the 2 valve.
Intake manifolds are unique the the cylinder head. Non Pi head has a non pi intake. The intake manifolds for the 5.4 engines are wider than the 4.6 so they do not readily swap. Adapters exist to fit a 4.6 intake on a 5.4 but it is easier to use the proper manifold.