Well I tested the battery again today and the alternator wasn't charging at all again. So I made up a new alternator cable straight from the alternator to the battery positive and the alternator is now charging! So it looks like it wasn't a bad alternator at all but a bad cable/fusible link.
I still can't get the old fusible link out to check and clean it (I suspect some water got in to where the cables plug in underneath as it was a bit wet under there) but I'll go to a wreckers soon and look at a fusible link box and try to work out how it all comes apart and try to repair it.
The new cable doesn't have an inline fuse so I might get one of these battery post fusible links below until I can repair the old one. Thanks for all the suggestions.
https://www.jaycar.com.au/battery-te...-100a/p/SF4182