If your car is a 64, the "factory module" isn't factory, it was added. I just removed mine and taped the wire where the previous owner had spliced into the harness for power. All the other wires go to either the distributor or the coil and they can be removed. If they did a nice job and taped them into the harness, you may have to untape the harness to get rid of them.
I guess you could leave the module and the wires in the car until you're satisfied you don't need them anymore. You would unplug the wires to the distributor when you pull out the old distributor. Also remove the wires that go from the ignition module to the coil and tape up all the ends so they don't short to ground accidentally.
After you've installed the new 12V low resistance coil, hook up the original wire that supplies voltage to the coil and short out the ballast resistor so the coil gets 12 volts all the time. Finally, connect the red and black wire from the new distributor to the coil.
That's it.