The ports are bigger and it flows better. The ports match the better flowing heads as well. Late 01-04 PI intakes are still plastic, but they have the aluminum crossover. The 96-00 intake is plastic with a plastic crossover. There aren't many of those around anymore.
they did, most who have a 96-98 w/ an alluminum x-over have the intake released by ford once they saw the problem. It's still NPI, if it was PI it'd need alteration plates or some well placed RTV. And if you bring your car in with a cracked manifold, the dealer/mechanic's computer will show a 99/01+ PI intake wont fit on your car so they'll charge you $450 for a new aluminum NPI
The PI intake is taller( height wise ) than a NPI intake. Also, the first runners go to the opposite side, I don't recall which goes where off the top of my head. Both of these are very noticeable differences. The aluminum crossover is not a good way to determine which intake you have. The improved NPI intake has an aluminum crossover, just like most of the 01+ PI intakes.
Scupking,
I doubt that Ford would replace your intake for free.
just adding on to what TGJ said, the PI intake has the first intake runner (front of engine bay) coming from the passenger side up and over then down to the driver side port for the head, while the NPI intake has this reversed.
here's mine: View attachment 342719