A common problem will be the moment when the magnet the hall will trigger.
If the magnet is to close to the hall, the triggertime will be differend when if the magnet is only 1 mm futher away.
Even if the speed change of the engine the ignitiontime will be changed too.
Test with a pulsgenerator is not the same if testing with a real engine.

@ Adrian, are your sparkcoils the same I mention into the link a few pages ago ?
I have also buy a very small grey ignition coil from Roy (S/S Machine & Engineering) but this coil didn't work at high rpm.
It quit at 6 or 8,000 rpm and didn't start again without switching off the power.

@ Charlie, have you try to compile the C-code with MicroC compiler like we do with our first CDI of JMJ ?