I had chance to have another look at this last night, from what I can tell the black wire which is currently connected at one end on the alternator should go to the thermo switch. I'll check more thoroughly later in the week but the only black wire I have connected to the relay is definitely currently connected to the alternator so not correct on that basis.
I'm still not sure about the black wire for the voltage regulator which does connect to the alternator - I know this is separate from the cooling wires but it is in the same physical location. Does anyone have a photo of where the three wires should connect on the regulator, I can only see two connections on mine with the black wire effectively connected to earth via the mounting bracket, then going to the alternator I think (not fully checked yet).
Also, many thanks to lancialulu for your time at the Classic Motor Show on Friday, it was good to meet you.