Try this.
Black Pertronix Wire to the Negative side of the coil.
Blue Ignition Wire and Red Pertronix wire to the Positive side of the coil.
Leave the Ballast Resistor connected as it was/has been.
^^^^^ This ^^^^^^^
If you have the red wire hooked to the wrong side of the ballast resistor, it's not gonna start.
Just looked at the Pertronix site and the Ignitor II has "reverse polarity and over current protection". That
should mean that if you hooked it up backwards, then
shouldn't be fried.
Pertronix has the instructions 100% correct. It is the easiest way to wire it. Optimally, you should be bypassing the ballast resistor, and that is easily done by putting a jumper wire between the two wires that hook to the ballast resistor. But that's not important right now as the car will still start with the ballast resistor in the circuit. Take any wires that you've added to the ballast resistor out and wire directly to the coil.
Here's how it works... We'll start at the ignition key. Turn it to the far right to start the car. That sends 12 volts directly to the coil. The car starts and you let the key off to "run" position. That sends 12 volts to the ballast resistor and the current runs through the ballast resistor to the ignition coil. When the current runs through the ballast resistor, it drops the amount of current down to make it easier on the coil and breaker points, but at the "start" position, we want as much current running to the coil as possible for the hottest spark.
So... Bypassing the ballast resistor is all good for your new Pertronix system in the ignition "run" position, but since you aren't starting at all, and the ballast isn't used when in the "start" position, that says it's just wired wrong.