OK, current plan is to solder some wires directly to the pins on the reg/rect, seal with silicone or similar, and then remove the connector from the loom and join the wires as per Bernard's mod. I'll let you know how it goes.

Incidentally, this would give the room to mount the reg upside down with the wires pointing down, but I can't see why this would be better. Any thoughts?

I've also discovered the 6D3 reg/rect is used mainly on Yam jet skis, up to 1100cc. Still no idea if it's a different spec though.

Thanks to all for the help/advice.