You can run gt40r with ballast(as per stock setup) and it will run perfect with Pertronix as it was designed as points drop in module and will run at 9v without any issues. If you want to run it at full system voltage you have to run appropriate resistance 12v coil such as recommended 3 ohm one.
R coil with ballast resistor/harness = 12v 3.0ohm coil
If you already have a new gt40r use it.
Cheers