My VX is supercharged. They perform very well eh, in fact it goes harder than our old 5 litre SS!
I'd recommend doing a cooling system overhaul - flush it out, new thermostat, new coolant etc. Simply because these engines can be a pain in the arse to work on and a dodgy cooling system will cause all sorts of problems, so it's worth getting that particular job out of the way early for peace of mind. The thermostat housing is located underneath the SC inlet and there's also a couple of bleed nipples through the system that you need to know about. I'd also go as far as to jack the front of the car up during the process as well - these engines will hoard a lot of air pockets so that'll help them all come up to the surface.
With the differential, you might just get away with re-sealing it and squeezing in some fresh 85W-140 LSD oil. Had a similar problem with my super six - it wasn't leaking but it was making a hell of a racket during tight turns (going in and out of my driveway and at intersections etc). So I just changed the oil and it's been quiet ever since.
The front end issue may go hand-in-hand with your brake issue. Commodore brake discs seem to warp easily over time which causes shuddering. Either fork out for a new pair or have them milled straight. It would pay to check the suspension, steering, tyres and wheels for warping as well. Given the dodgy panels you found it most likely has been pranged on that side. After those checks, go and get a wheel alignment. In fact, the tyre guys could probably check out the underbody for ya while they're at it.
With your AC, as you said just have a gander at the wiring. Another thing to keep in mind is that with a vehicle this old the AC system might have had some of the refrigerant escape out of it over the years. So even if the compressor is functional you may not get that cool refreshing air that you roasting aussies desperately need
As for the rest of the work like your seat and exterior rubbers, it's pretty self-explanatory. Just remember to disconnect the battery if you're planning on yanking out the seats. There's usually seatbelt pre-tensioners as part of the SRS systems. Disconnecting the battery will avoid the airbag light staying on after you've disconnected and reconnected the seat plug.
Happy hunting, mate