G'day AJ! Am I right in thinking that you bought your sunraysia wheels off me? Good to hear that they may be going onto a proper baja to really make the most of them!
You should have no legal issues with building a baja out of a '69 beetle. Fibreglass fenders and other bolt-on panels are perfectly fine as long as they have no sharp projections sticking out of them to impale pedestrians. The National Code of Practice for Light Vehicle Modifications says that all fibreglass panels should be a minimum of 3.5mm thick, but I doubt that anyone would test you on this unless your panels were flopping around all over the place. Fibreglass fenders, bonnets and so forth are all legal without a certificate.
The only issues which you would have are the legality of moving lights and/or changing them for different ones, plus the actual cutting of the body in structural areas and hence protecting people from the spinning parts of the engine. If you change any of the lights, make sure that your new ones are ADR approved and clearly visible from the front/rear and side of the vehicle. There are special regulations for the range of angles which lights need to be visible, but as long as you use some common sense there's nothing much to worry about.
If you cut the rear of the body then a good cage which covers the generator belt/pulley and the hot exhaust would be a good idea. If you cut the front or rear of the body for the kit, then I suppose it should technically probably have an engineering certificate, as these are structural (ish) panels. I would personally just build it properly and in a safe fashion, then not worry about telling the rego authorities. If you really want to do it properly then any engineer should easily give you a certificate for a normal baja kit, as they're at least as strong as the original body, and the sections of the body in front of the beam and behind the rear suspension mounts don't really do very much structurally.
Here's some light reading for you to give you a general idea:
http://www.infrastructure.gov.au/roads/vehicle_regulation/bulletin/vsb_ncop.aspx
Most of what you want will be in the sections of Body and Suspension.