Does anyone know whether it's ok to leave the factory connector on the alt (that goes to pcm) and just add the new wires to the alt terminals that will go to the external regulator? the reason I will leave the original wiring harness in place is because my pcm issues stop when the weather warms up and without it I don't have act or cruise control. Am I missing something? Don't want to go back to gas but this is a pain in my a**. 1993 D350

You can leave the stock wiring to the alternator attached but the green wire will most likely require to be cut going back to the PCM. The blue wire is the +12V for the regulator but the green shouldn't have any other contact with other devices but the alternator and the live regulator.

http://articles.mopar1973man.com/general-cummins/34-engine-system/134-voltage-regulator-mod