As CDI box #1 feed the #1 and #2 cylinder and box #2 feed the #3 and #4 cylinder I suspect the blocking diod in CDI box #1.
The wire you disconnected for the stator is feeding #1 CDI box.
If you swap the CDI boxes the spark at all cylinders will occur if you disconnect the #3 brow/black/blue wire if it is something wrong in the CDI box..