Gr8,
I think you may be getting a little mixed up there.Circuit diagram clearly shows that when using the unit as CDI, emitter Q2 is connected to ground through 1k0 resistor with the collector connected directly to the positive rail.
When using it to pulse a transistor ignition, the collectorof Q2 is connected to the positive rail through 1k0 resistor with the emitter connected directly to ground.
If I remember my theory from 30 odd years ago, the former is common collector and the latter is common emitter configuration.
Basically, with the pulse from the micro, the CDI and the Transistor power stages require inverse signals.
Anyhow, you nutted it out in the end so good work there. Hope to get time myself for some results shortly.
Cheers .....Jeff