The routing of the wires you describe is weird. It's been a long time since I played with my Pertronix, so I'm not sure if the module has polarity stamped on it. I do know that over the years the wiring colors have changed since I have seen one with white and black, but I can't see them using red for anything other than positive.
Go to the Pertronix site and download the instruction sheet for model 1281. That will give you the wiring setup. It sounds like your setup might have retained the resistor in the circuit, which is more complicated than it has to be. You need a 12 volt source that is switched, eg on only when the key is. The easiest access is to splice into the switched wire at the voltage regulator. On a 64 it's green/red, but yours looks like a 65, so I'm not sure of the color. Easy to check, 12 volts when engine running, nothing when off. That wire goes to the positive side of the coil and the Pertronix module goes red to positive and black to negative.
That should be it. If there was still a resistance in the 12 volt feed to the coil, the Pertronix wouldn't work properly but you would still have had spark.
I think trying to sort wiring out and go back to the old points would be tough given the layout you've described. Modules are available everywhere.
Terry
64HT
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