Hi Mick,
Is it really a one wire or is it a three wire which is sometimes called a one wire, probably because it has an inbuilt regulator?
I'd be surprised if you put a one wire in, you won't have an ignition (dash) light with a true one wire alternator.
So, does it have a socket on the outside of the casting, maybe with a black plastic plug in it, as well as a stud/nut at the back?
Need to find out a bit more about what you've got before thinking about the immobiliser problem. It all sounds a bit strange.
Bob