I know in Tasmania you can do this conversion without any engineering certificate or anything. You only need to change the engine number with transport. And maybe have a $20 inspection to verify the new engine number and general roadworthy of the change. Nothing special. I know with my KE35, and can fit any Toyota engine up to 1600cc. Only need better shocks and front brakes of a cirtain diameter (not very big).
If it was me, I would only change the engine number on your rego. Tell them its basicaly the same engine (which it is).