When you contact the RTA, dont identify yourself and your car until you have all the answers you need. That way if it could potentially become a nightmare you could always do the dodgy and chase down a set of compliance plates from a wrecked one. (Not that I would suggest that this is the best route, just that you could, if you get desperate, go down this path)

From my experience, as far the the licenseing dept is concerned, old cars tend to get all sorts of things mixed up, so that will usually just get you to fill out some extra forms.
A HR holden that we licensed a few years back after a resto, we found out was reported stolen in the early 80s. They just changed the name on the papers and did the inspection. NO sweat.