i have a supercharged 00 mustang gt.   I plan in the next year or two, on buying a crate engine with forged internals, i beleive that a 5.4 would be a direct replacement, for the 4.6. is it a good idea to go with the 5.4, or is there complications involved with the swap. do the 4.6 heads bolt on the 5.4, same bellhousing?  what are the differences, i know the cams are the same.  

The bellhousing and heads bolt right on.  You'll have to deal with a huge engine height that probably will not fit under even a 4 inch cowl hood.  You'll also need to reprogram the computer for the added displacement and a set of headers/pipes to go with it too.  But it'd be awesome once done.  

as you may already know with the 4.6 to 5.4 engine swap alot of the parts are similar. but the biggest problem is clearence. i found that one thing you can do is to get an intake from a full size van that also has a 5.4 in it. this intake has a lower clearence and will help free up some extra room.  

intakes are about to be available for mustangs with 5.4 2v's. Should fit under a stock hood.

www.hiperformancesolutions.com/54.html  

Save your self a whole lot of trouble and just buy a good 4.6 like Ford Racing's Aluminator short-block. they're good to over 1000hp.  

I have a 2004 Body in white and installed a 5.4
Navi long block into it,
and it fits under a stock Mustang GT hood.
I used the Aussie Boss 290 lower,
and modified an Aussie upper intake.
It puts the throttle body in the stock
99-01 Cobra/ 03-04 Mach 1 position.
It uses the stock P/S hoses, AC hoses, throttle
and cruise control cables,
and basically 99% factory Ford parts.
Stock crossmember is in the car.
No cutting or bashing of the body is needed.
Steve, I met you at Steeda a few times and at
Sebring for the Camp Steeda event.
Pics are at th Mach 1 registry under
the general registry discussion headig,
and labeled at "new Project "R" thread.