EDIT
Solved the problem, if the battery is really dead, the Reg doesn't output a decent voltage. While its running if I connect another battery with jumper cables the voltage goes up from 12.9~13.2 up to over 14v.

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Alternator is putting out good power, it easily runs a halogen bulb on either winding.
Reg puts out 14v. But the battery hardly sees 13v.

If I unplug the Reg's output and measure the resistance of either red wire to the 4 pin terminal with the fuse next to the battery, I get 0.00 ohms. But neither of the green wires have continuity between the Reg output plug and the 4 pin terminal fuse thing next to the battery.

The 2 green wires at the Reg output are solid green. and the 2 wires at the 4 pin fuse terminal are green with a red stripe.

From the NC30 wiring diagram it looks like the green wires from the Reg output run to the switch, and from there they get connected to frame ground.

I recently bent some wires near the ignition to free up handlebar movement, so I've likely damaged something there.

your battery might be no good, get an autoshop to load test it.

the green are earth cables. Check them to the frame.

I think those green cables that run from the Reg output get switched to ground when the ignition is on, the NC30 wiring diagram shows this. The charging system makes good juice when a good battery is connected.
The battery was completely F'd. Charged it all night and in the morning after disconnecting it for a few mins it sat at 10.5v indicating a dead cell. Gonna try claim warranty.

Lope wrote:I think those green cables that run from the Reg output get switched to ground when the ignition is on, the NC30 wiring diagram shows this.

Your bike is NOT an NC30, it is a different bike so the wiring diagram is no good. They are very different bikes! Like when you try and use the NC30 diagram for your cable routing and carbs, the NC30 one is no good either.

http://www.jacksons-lair.co.uk/nc24wire.jpg" onclick="window.open(this.href);return false;

The NC24 wiring diagram can be seen above. The green wire on both my 24 reg recs is always grounded.

Thanks mate!