Yes, it can be done, and as posted above it will take a good chunk of change.
If you are looking to drop in a 5.4, then a 5.4 3v is a great way to go if you don't want to spend the money on a GT500 engine. You can pick up the 5.4 3v fairly cheaply, but you are also talking about new trans, wiring harness/comp and a ton of peripheral parts that add up fast.
Your best bet is to talk to a performance shop that knows what they are doing and partner up with them to help map the way.
A rough price to do a 5.4 3v is 15k, but obviously a lot depends on what you spend on the engine and trans.

 

It can be done... but buying a GT outright would be less expensive if you want to go the 4.6 route.

 

heck, with all the money you would be spending you could ALMOST buy a used gt500 if you sold your 6er and got a good bit for it

 

Well money aside, I really approve about engine swaps successfully done...
Folks like buckman are the sh#t. Make a sixer go fast and then put a totally different set-up.
Nothing conventional.
I like that.

 

What about getting a built 4.6 3v like the one that livernois offers and then throwin on the ST Motorsport's whipple supercharger kit that uses the 3.4L whipple that can be used on the GT500? That'd be a lot cheaper and you could still have a CRAZY fast car and those are rated up to 1,000hp...if you want more then you could switch out to another block on down the road...