We finally sussed out what was going on!

After spending ages studying wiring diagrams we concluded that the connector would've been part of the air con system.

It wouldve been an optional extra from fords so the wiring is there and should've had blanking plugs in the connectors.

I wont go into details but a new water temp sensor has sorted the problem

Now all I gotta do is kick sis's boyfriends arse for not mentioning any of this before i went out and bought a new altenator!