The Air filter setup and MAF setup are different. Not sure about the exhaust. The gen 2 3.0 has the plastic flat type air filter box with a diffent type of MAF sensor behind it. Not sure but I remember reading that this updated intake is what increased the HP.

99 Gen 2.5, fixing blown head gasket
89 SWB- 33's, ARB Front locker, SR rear locker/axle, SR F brakes, winch, WST Offroad Armor all Around, 2.85 Aussie T-case Gears (SOLD)
Sold: (2) 95 SR's, 86 SWB, 90LWB, 91 LWB
-Can Change a timing belt in my sleep..