The 2nd Gen Lightnings used a 5.4L single overhead cam/2 valve head just like the regular F150 truck motors, although they received bottom end attention, different cam profiles, and maybe even some head work (not sure about that one) to accomondate the blower. As far as the blocks, the 4.6 and 5.4 are different (deck height), but since 1996 when they first found their way, I don't think there have been many changes. The Cobras did have an aluminum version until 2003 when they got blown
. The 'modular' blocks are very, very strong....unlike my 5.0 block
.
Edit: No mustang or cobra has ever came from the factory with a 2 valve 5.4L