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The heads bolt up, but the wiring and electronics are not there for the drive by wire throttlebody or the variable cam timing of the 3V and you will also need to do alot of fabricating to do the 4V thing as well.
The Mustang Supercharger will not bolt to 2V heads. It also puts the TB on the wrong side.
Your best bet would be a Lightning 5.4L.
If you're referring to an inlet tube-don't waste you time-NONE of the aftermarket pieces will net you any HP gain-the entire intake manifold is the problem. You could swap a Mustang intake onto it with a bit of fabrication for fuel rails,etc....but you'll lose a bit of torque down low due to the design of the car intake.
JL
What about a supercharger? The 5.4L is supposed to be a 90 Degree engine so I can't use one from the lightning, can I? So what can I pirate one from?
The block configuration for the 5.4L is identical as a 4.6L,it just has a taller deck(so the Lightning S/C would not fit)-similar to an old 5.0L vs a 5.8L. You can use several S/C kits-just about anything for a 4.6L 2V engine will work.You'll have to do some fabricating to get some of them to fit right. Vortech and Paxton both make kits for the 4.6L trucks,and there are also some positive displacement S/C companies that make kits for the trucks too. It's all based on what you wanna do. I've got a Roush Stage 3 intercooled S/C kit for sale on eBay right now-I was gonna use it on my '98 model before Dad bought it-just never had the time to do it.It's for a Mustang,but would work fine on any 2V with minor fabrication.
JL
I talked to the guys at BBK, and about 6 months from now they are coming out with an SSI & DSI Intake for the 06' 4.6L 2V SOHC
Don't hold your breath-several companies have been promising intakes for the 4.6L's for a LONG time now,and so far only Edelbrock has produced,and the only one they have available is the Victor Carburetor version.
JL