Wow, that is quite a story about the new pack. My guess would also be a connection problem, but perhaps the new pack may not be as sensitive to the stator voltage or the triggering voltage as the old pack. A lower stator output that was still in spec could keep one bank of the pack from firing. You would need a ‘scope to watch the voltage waveforms going into the pack. Can’t remember which side of your motor that the shift switch cuts out – they changed over the years – so unplug it and remove the ground terminal and see if spark returns. Any resistance through the shift switch could lower or bleed off the internal voltage for the one bank.
Can you fabricate a way to swap the 2 stator charge coil leads to see if one side follows with no-spark? Those will be the brown and/or brown-and-stripe wires from the stator. Bottom line, it's probably the stator - as you know, components can check good but not work correctly and the one charge coil is lower than the other.
If you pull the flywheel, I'll bet you will find a puddle of melted insulation under at least on charge coil. That means someone had wing nuts or loose battery connections that affected the regulator and that in turn overheated the stator to the point of melting plastic.