To answer your question directly, yes the 4.6 should swap easily into that car because it's factory installed.
However, it really doesn't make sense to install a 4.6 in a '99 V6 car. First, there is much more to making the swap work than just dropping in the engine. You have to completely change all the wiring and computer to even make the engine fire. Also consider that the transmission (I don't even know if it will bolt up) and rear axle will not hold up to the 4.6. Not to mention that the 4.6 is relatively expensive as far as engines go, GT's are relatively cheap, and changing the engine would completely destroy it's value (unless you put in a fire breathing pushrod motor
).
If your friend want's a 4.6 in his car, then it would be much cheaper and far better to sell it and buy a GT.
------------------
2000 GT --
Black, 5sp, Mach460, Bassani CatBack & X-Pipe, MAC Cold Air, 70mm Tbody, Hurst Shifter
1966 Mustang Coupe --
Tahoe Turquoise, Pony Int, A-Code, C4 Auto
------------------
scott@pearland.com