I took the decision to bite the bullet, and have sent the entire ignition system to Steve at Bradford windings for assessment and repair. When I spoke and mentioned the running backwards issue, he suggested that pointed towards the timing sensors.
It was going to involve a 20 mile trip to find a suitable pull up resistor, and even if I had tested it, I then have the issue of where to go next regarding fixing it. If it was the hall effect sensors, sourcing them isn't easy and de-potting and replacing with my equipment looks tricky. If they are working fine then I have the issue of a new or refurbished cdi unit. Hopefully I'll have it back and running within a fortnight.