Tranny changed from 5 to 6 speed in '04, which may affect the ECU. It's also a different type of engine in regard to things that would happen if your timing belt broke, IIRC.

Better to be safe and match the engine with the model year series ('04-06), if you can.

 

in regards to the timing belt. When the older Ls400 changed to Vvti heads a decade earlier is when the engine went from non-interference to an interference fit. Ls430 engines all interference design so a broken timing belt is bad news.

For the OP, I would recommend having both engines side by side and transfer the entire engine loom over, potentially any sensors and belt driven accessories changed over as there are minor electronic differences. Keep your original transmission, ecu and wiring loom. The short engine block, heads and intake plenum are mostly the same from what I've seen. its the sensors ( including the throttle body) and things like that can change mid life. I know the alternator is one accessory that is different. You would have to get an online parts diagram (I use http://www.japan-parts.eu) and compare both engine bits side by side to see a part number change. Some updated parts are compatible and some are not.. Certainly doable if you're stuck but getting the correct engine would be my first choice if you want to do an easy changeover.

 

I did an engine swap for my kids this last summer. Daughter blew the engine on their Cherokee. It's a 95 with the old 318 in it. I found a 96 and did the engine swap.

Due to the one year difference in in model years it about doubled the amount of work to do. Only thing I could use from the 96 was the long block. It is far easier to do the task like the manufacturer does it. the entire package, engine, transmission and engine harness. In my case Jeep went to OBD 2 in 96, thus the harness and electronics were very different.