The module will come with the instructions on whether or not to run a 12v source. I know for sure that the igniter II can be ran on 12v or the ballast resister, it's opional. I did do a test when I installed my igniter II ,and the old resister wire on my 64 Ranchero dropped the voltage down to 3.84 volts. All you have to do is unplug the wire from the ignition switch and replace it with regulare fine strand wire, I used 14 gauge probably much bigger than needed. On 64/65 Falcons/Rancheros the wire is pink with a white stripe; I'm sure that mustangs, fairlanes, commets are the same it would only make sense.
I would not expect any performance gains with the stock coil. The Flame-thrower II coil is designed to run on 12v and has a low ohm rating of only .08 ohm. The tiny distributor cap is unable to handle the full potential of the 45,000 volt Flame-thrower II coil and I would also assume the same for the 40,000 volt Flame-thrower coil. When the plugs are gapped greater than .050 the spark energy will arc to the cap hold-down clamps, I know this from experience. Now if you are that extreme this can be corrected by slathering dielectic grease all over the cap, and you probably wont notice any increased performance if at all. For the just in case emergency you should carry the old set of points in your vehicle with at least a screw driver and a 3/8 wrench to install them; if you are running 12v to the coil or just to the module I recomend also carrying a spare ballast resitor though you can run 12v to your points but they wont last to long.