Pertronix III set up

1.........As usual let's start with "what are you working on?" Year make and model. Wiring changes colors through the years, and yours looks a bit "hacked"

2...DO YOU have and if you do not, GET a wiring diagram/ shop manual. You can download these for many years up through 73 for free, over at MyMopar

3...DO YOU have a test light, multimeter, and some alligator clip jumper leads? These are must haves for doing any electrical work on these cars

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I'm assuming your display of the coil primary wires is suggesting you lost which one is pos and which is NEG. Unplug the big connector at the OEM ignition box, turn the key to "run" and see which wire is hot. That is your coil +

What used to be coil NEG goes back to the OEM box and will not be used

Ballast..........disconnect all wires from the ballast. Turn the key to "run" and see which two are live. Those are actually jumpered together and are in effect one terminal point. Take one of those live wires. Jumper from one of them to first one and then the other of the remaining two wires. Put your test light/ or meter on the coil + wire. When it is hot, that is the correct connection.

The remaining wire went back to the OEM box and is not used.