This really seems like the simplest solution and the way I would attack it. rock up with the hard top and seats and let him sort it out.
When I took mine in for rego (QLD) I was told that mine couldnt be a wagon as it only has 2 seats. I showed her a picture and she agreed it certainly was a wagon. she walked off, added 2 seat wagon option to the system and carried on with the paperwork.
I really feel for you mate! :(

