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Depends on how the bike is normally setup. The IGNITION output from the M-Unit is just for power. So if your bike has points, the points wires are still needed. If your bike is a TCI, it's the same deal. Negative side of the coils still goes to the ignition unit.
For a CDI system, I prefer just to skip the M-Unit for that portion, but you can include an additional NC relay that ground the CDI box when power is off.