Personally i would definately go for the aftermarket EFI (because i like projects )
If you're worried about beinf screwed over emissions the best thing to do is to just give the RTA in your state a call and ask them.
Persuade them you're not a 'hoon kid' and you have respect for the law and the RTA by talking with them about your aims and ideas, for example:
Benefits over the carby setup...
- More fuel efficient
- Cleaner running
- Smoother
Mention too that all of the original emissions control gear will be fitted for the engines new life aswell.
Then ask them weather a simple 5 gas 'abbreviated' emissions test will be satisfactory.
If all else fails then do it, make it look sort of stock (no shiny polished pipes and blue hoses) and dont tell them a thing, then just stay under the defect radar.