Apologies for being unclear, what I meant was the engine sounds fine until the horrible grinding noise came in from the transmission area. Regarding the 12v battery issue, I'd read up on it and the thermistor was placed on the new battery at the time. So to clarify the above, previously the car would go to "ready" mode, then engine would turn on and approx 2-3 seconds later, the check EBC and check VSC warnings would show up and the car would stop running accompanied by some grinding noise from the transmission tunnel area.
Since posting this thread, I have read this excellent thread: GS450h Loss of Power which describes a pump in the area of the noise I was hearing and a friend came over with a scan tool. The only code the car would produce in the generic sealey scan tool was P3191 which just means "engine did not start". We decided to try and start the car and low and behold it started perfectly, but not without a very short grindy noise from the transmission area, then just a consistent mechanical light clicking noise. Car is currently charging and running perfectly with no errors. I will go out and check it again once it has cooled down again.
So I believe my issue is the transmission motor pump unless anyone has any other suggestions?