Mooohahahaha, That's it fixed, blue core going to the fan control box was broken just above the plug, looks like water got in, an aircon top up and it is as good as new.
Thanks everyone for you help, now all I need to fix is the faulty passenger door window switch and speaker, gearbox and engine mounts, sticking rear brakes and squealing front ones..... Bit like triggers brush!
To recap then, going to the fan controller 6 pin plug on pin 1 is 12v when the engine is running, pin 3 is then grounded by either the aircon control or engine thermostat, this sets the fan to run at stage 1. Then pin 5 is grounded as per pin 3 / stage 1 but at a higher aircon demand or higher engine temperature this sets the fan speed to stage 2. Thus if you put 12v to pin 1 and ground pin 3/5 the fan should run, proving the controller.
There is is a constant 12 v supply to the fan controller which is fed from a large fuse above the normal fuse box (requires lower dash removed to access)
The fan controller then takes the 12 v feed and sets the output to he fan at either none, stage 1 or stage 2 dependant on the input
Using vcds you can test the fan output but if your aircon pressure is low this will not work, thus the test fire is done through the hvac system and not the engine or instruments which I thought strange.