Hi Jack,
It would be worth talking to Peter Ransom at DRB / GT40 Australia about this - I have heard that he is starting a new batch of GT40's, and that one of them might be a "turnkey" with the 5.4L. Given that, he will have to solve the emissions scenario, and all other builders should be able to piggy-back on his solution.
My understanding is that to get an "automatic tick" for emissions, you need to run a stock motor with stock ECU & "equivalent CAT's". The trick is to bypass all the normal "body computer" inputs so that the thing will run, & I have heard that this has now been done.
PR will be able to give you the details.
You will have heard a lot of theories about how to select a car - start with the HP & transmission / body accuracy / space frame vs mono, etc.
BUT in Oz, there is one overriding factor for rego - emissions. The best starting point is a good "certifying engineer" who knows the rules - in NSW, Forum member Trevor Booth is the man. He may be able to help with Vic (or recommend a local guy), but this has to be the starting point.
Half a day's worth of consulting fees for a top certifying engineer will be the best investment you can make - without my half day with Trevor at the outset of the project, I would still be trying to get it registered.
In terms of sourcing a 5.4, Trevor, the local engineer, or Peter Ransom will be the best source of info - note that you will need the engine plus its original ECU (and all the numbers must match so that it can be proven to have come from an Aus registered car - US crate engines are a big problem as they do not generally have engine numbers, or have ones which do not necessarily prove that they came from an acceptable vehicle).
Hope this helps a bit.
Kind Regards,
Peter D.