The number, and size of the bolts that hold the upper intake onto the lower intake is different. The 98-00 had 6 bolts that I think were 8mm. The 01 had 6 bolts that were 6mm, and the 02 had 4 6mm bolts. (I'm just going from memory on the sizes, so I could be wrong on the exact sizes, but the 02 mounting bolts are definitely smaller than the 98-00)
To put the aluminum upper from a 98-00 onto the 02 lower, you'd have to drill/tap the lower intake for the larger diameter bolts. If you want to put the composite upper onto the older lower intake, you'd have to drill and tap the upper intake mounting holes. And you'd have to figure out a way to mount the coil pack since there's no way to mount it directly to the composite upper intake.
What you can do, is swap both the lower and upper from your truck onto the newer engine, and you wouldn't have to drill/tap anything. Put fresh intake gaskets on while you're at it.