After squaring my bike away with all its problems.... now the alternator has packed in. Two out of the 3 cables are getting power.

Is it a dear do?

Not a dear do - can get a second hand genny/alternator from someone on here I am sure. Gasket and 20 mins..sorted.

How did you determine that the stator is faulty?

I'm checking through it all today to find out exactly which bit isn't working.
What should I check? 2 out of the 3 cables are getting power so i'm checking continuity in the one that doesn't. After that i'm not sure what else to check.

The bikes been stood for 12 years and it was charging last week, I checked it twice.

Measure the resistance of all three yellow wire relative to each other, A-B, B-C and C-A, should measure 2 ohms or less. Also measure the resistance from the yellow wires to chassis, should be infinite.