You have a car with a non standard engine fitted.
If this were done in SA, in order to get it registered with that engine, you would have to prove it complied with the emissions standards applicable to that vehicle.
It's one of the perils of doing engine swaps unfortunately.
What car did the current engine come out of?
If this car was sold in Australia, then there would be emissions data for the STOCK engine (including stock intake and exhaust) that may satisfy the requirements.
If not, it will be very hard and costly.
What's the car worth?
I'd say you're looking at the best part of $10k to get it on the road in SA unfortunately.
Possibly the easiest/cheapest way would be to buy another stock one, swap all the bits over to get it on the road, then go from there.