personally i think it depends on what you want to do with the car. if you want to build a badass N/A car then the 5.0 is the way to go
turbo/supercharged i would go with the 4.6. with the right internals the block is said to handle 1000hp+
if you wanted a 96-98 4.6 you can do the PI swap and have the same HP as the 99-04 gt's. also if you shop around the PI swap can be done for cheap
the DOHC 4.6 is a sweet motor
interior from 94-04 is basically the same with only minor changes (color options, cupholder design and seat design)
orrrrrrrrrr you can buy a rolling chasis and swap in a LS1. a guy on here with a fox did it not to long ago
turbo/supercharged i would go with the 4.6. with the right internals the block is said to handle 1000hp+
if you wanted a 96-98 4.6 you can do the PI swap and have the same HP as the 99-04 gt's. also if you shop around the PI swap can be done for cheap
the DOHC 4.6 is a sweet motor
interior from 94-04 is basically the same with only minor changes (color options, cupholder design and seat design)
orrrrrrrrrr you can buy a rolling chasis and swap in a LS1. a guy on here with a fox did it not to long ago