6.1 hemi 6013 msd

Not sure what you mean about wiring into the factory harness?

The MSD harness is a stand alone ignition harness that is plugged into the 6013 ECU.

The ECU harness also has provision to be connected to 12V constant, 12v switched and an earth from memory -

Its not designed to be used with the factory PCM...it assumes you are either using a carb or an aftermarket EFI controller.