Pertronix III set up

To get rid of everything completely couldn't I just follow all of the ballast wires and eliminate them from the harness along with the factory ignition box and all of its wiring and all I would have to do is run that wire that is hot in the start position which was the brown one to the positive side of the coil.

I have attempted to explain. You go "eliminating all wires" and you will find there are other things "in there" the no longer work. Like, maybe, the alternator.

Let me put this another way........start "backwards" from the ECU connector (igntion box) Carefully untape as you go from the ignition box towards the ballast. Eliminate wiring hooked to the ECU. If you come across an in harness splice do NOT eliminate from there "forward." Then splice what's left all together at the ballast.