Welcome to Gpf, where your questions usually Ger answered with a link...lol.
Lemme try to help...
First off, let's get some terminology right. The gen2 engine is known as the L67, the gen3 as the L32. The reason we don't use "Gen" to refer to the different engines is because that term is commonly used to describe the superchargers on this engine. Your L67 came equipped with what we can a gen3 Eaton supercharger. Where as your L32 came with a gen5 Eaton.
you will need to find an adapter plate for ur l67 throttle body to bolt up to the L32 supercharger. Or you can upgrade to an ls1 of northstar throttle body.....all requiring an adapter plate. The reason u can't use the gen3 TB is that its drive by wire...
Also fueling needs some changes too. The 04 is a return less system, therefore the fuel rail from the 04 will have to be swapped with your 97-03. Additionally, the fuel injectors on the L32 have different connections, so u will need to swap injectors also.
Vacuum system also needs some tweeking....look up my "Gen v supercharger thread" for some detailed info on what u need to do for that.
Wiring should be pretty plug and play...I do believe the engine temp sensor in the lim was changed, so u may need to swap out that sensor as well.
That's all I can really think of off the top of my bead. Hopefully others will chime in with more useful information....and no more links.
Sent from my sweet DROID Razr Maxx