im in SA and i have done a few of these conversions.
The way i understand it is that if that model of car was released with that engine and you use all the emission components that the car requires then you 'should' be fine.
VR was released with a 5L v8 so you can use any of the efi 5L engines. We even did a VT HSV 5L into my mates VR and it was approved with the new engine number, without inspection, no worries. Ive taken a efi 5L out of my VN, put a manual behind it, and slotted it into a VR using VR 5L loom and ecu. applied for the engine number change, and was passed by regency for the engine number no worries.
In terms of brakes... if the defect was for changing them i.e. fitting VT brakes, then yes thats a defect. Suspension... well they are well within their right to issue a defect on that. I assume that you lowered it? its a modification that is outside of the factory specs. so its defective according to them. stupid i know...
Pretty much they can defect you for anything on any car, even if it just suspicion, and its your problem to prove that it isn't. thats the unfortunate truth that many of us encounter.
From the info u have given i dont see why they defected you? but there could be more to your story?
Were u speeding? or doing any hoon like stuff? cause that usually is a good excuse/ opportunity for a cop to slap a defect on a car