Talk to an engineer is your best bet. They are the ones who need to certify any changes like this.
I haven't done the swap but your questions are largely based around legislative requirements and a rough idea follows.
Going to an older engine might be tricky but check the applicable ADR's for emissions. If they happen to be the same for both vehicles, use the complete airbox to exhaust manifold setup as in the donor car. Most engineers will accept factory setups.
That said in 1999 the government started to introduce euro 2 and 3 equivalents for new cars. JZX100 was 1998? you say your IS200 is 2005. So a straight swap based on established compliance is problematic and you might be up for trying to pass an emissions test. You might be able to show that JDM emissions standards met or exceeded Australian standards in 1998 and comply with ADRs applicable in 2005 (Was there an ADM 1jz powered car in the period that you could blag your way through with?)
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