Thx again Andy,
We ran a further test to check the function of the mini sensor. With a breakout chord connected between the input plug and the box we rotated the flywheel around and measured the voltage across the various parts of the plug. The lower sensor's A channel dropped from 5v to (virtually) zero at the appropriate time. The B channel's voltage didn't change throughout the entire rotational cycle.
We also checked the spark generated by the coils and when on the R side the appropriate coil did not fire either (which stands to reason).
Given that we had previously swapped the L box for the R box and the problem remained on the R side that really confirms an input (rather than output) problem and the above test would pretty much confirm a problem with the lower sensor B channel (sensor or wiring). Rather than spend many more dollars fault finding I've ordered a replacement sensor from Cub Crafters USD250.
I truly hope this solves the problem. I think it will but it has been a crafty gremlin so who knows..
Cheers,
James.