One way to compensate for the resistance in the car's primary wire is to buy a coil with less primary resistance eliminating any re-wiring.
The pertronix pickup needs to be used with the correct ignition coil resulting in the correct resistance in the primary circuit. A pertronix technician will be able to guide you in choosing the right coil.
If memory serves me, I had to replace a 3 ohm Mallory coil with a 1.5 ohm coil in my stock 68 but then my memory kinda sucks these days.
Mike.