I know they'll bolt on to a 4.6 block, but the manifolds for either the 4.6 or 5.4 will not if I'm not mistaken. I think the 4.6's have a bigger gap inbetween the intake runners than the 5.4's do. Don't quote me on this though.
This is the best info I can find on the subject. FR500 Heads or Port Stock - SVTPerformance
EDIT: I have also heard that the Ford GT/GT500 heads flow a little bit to well for the 4.6's displacement, atleast for a streetcar. Again I don't know this to be fact just what I've read from researching this topic before.