Ok, so using the workshop manual you can carefully trace the route of the loom, so starting at the mid-point for the indicator relay/ rectifier and connected the wires that directly plum in to the motor I worked backwards to the rear light. Once I had the loom in place I re-fitted the rear light assembly and connected the wires to the loom. Next I re-fitted both the rear mudguard parts and bolted on the CDI, Rectifier and Indicator relay.
The next job is to get the oil and coolant reservoir, batter box and air box in place, so these all came to work for a scrub in the parts washer.
Tip: The owner’s manual doesn’t tell you how to do jobs like ‘fit the rear mudguard’ so its supper handy to also have the exploded parts diagram handy so you can see which part goes where and with what bolt.