Hi all,
Sorry for not responding earlier. I’ve spent some time cleaning up all the connections to the battery/fuse (those aftermarket fuse holders from Yambits are cr4p) before I start the bike up again and check voltages etc.
Now, I’ve seen the post from Akara1 about a ‘missing’ wire…
I’ve just checked my bike and yes, there are 3 wires on the harness side of the connector and only 2 wires on the Rex kit (nothing to connect to the green/red stripe wire).
Is it really as simple as linking the green/red stripe and green/white stripe together?
How did you find out about that? Did you call Rex’s? or see it as a fix somewhere else? or was it clear on the fitting instructions and I’ve just missed it…
Will it cause any damage linking the wires together?
I wonder why the Rex system has only one charging circuit when the original Yamaha system has two?
Any ideas?
Thanks for all your help…. 

I had just figured it out based on the theory of the wiring, I haven't heard anything from Rex about it.
I assume it's because Rex's speed shop is based out of UK, and UK model bikes may have had an always-running headlight instead of the on-off switch we got on the early US models.
Rex might not be aware of the wiring difference for the early USA model bikes so you'll have to add the wire youselfif you don't have a spade terminal you can just splice the green wires together on the bike harness side.
the original purpose of two separate circuits for the lighting is that serve as a crude method of voltage regulation and to prevent overcharging of the 6v system when the lights are off.
Rex's 12v kit includes a real voltage regulator for charging so you don't have to worry about the dual lighting circuit nonsense.
hope that makes sensesplice the green wires so all 3 connect together

Thanks for all that.
I’m going to copy what you’ve done ie, modify the Rex wiring rather than the bikes original harness.