crane fireball hook up

Decided to clean all the wires up in engine bay. I am also doing the mad wiring upgrade. The question I have is I was running a mopar electronic ignition box and distrubutor. I would like to completely eliminate the ballast from engine bay and the old mopar box, when I unhook the box do I have to leave the old part of this harness, if not where would the distributor wires get hooked up too. I have the center bulk head disconnected and lots a tough wires, so I have cut these all back to bulk head, going to run all new wires from there on. And did the mad wiring for three of the five that I have left after cutting back flush the ones that will not be used, such as oil,temp and brake. I have a brown and blue that branches off to the ballast. How do I wire all this. Thanks