THe 4.6 originated in the mark VIII and lincoln town cars. In the town cars it was the sohc version, in the mark VIII it was the dohc. THe 5.4 and 4.6 has much the same realtionship as the 302 and 351. All the same parts fit, but the 5.4 has a taller deck height and longer stroke..but the same bore. You CAN interchange all the heads from all the blocks wether it be 4.6, 5.4, sohc or dohc.
The 4.6 in the explorer IS NOT the same engine in the cobra. The cobra is an aluminum block dohc engine, the explorer has an iron block sohc engine.
5.4s are found in f-series, expeditions, and excursions and are all the sohc variety. the only place you can find a dohc 5.4 is in a lincoln navigator. In fact, the dohc 5.4 found in the cobra r uses modified navigator heads. This engine made 385hp and torque. THe lightning uses a sohc supercharged engine with an iron block and makes 385hp and 450tq.
The GT-40 engine is a 5.4 dohc engine with aluminum block and heads and a supercharger. It is PLENTY capable of making 500hp and 500tq...in fact, im positive if you slap on aftermarket goodies itll make even more.