Which Pertronix model and which coil have you installed?
In all cases, the Pertronix Ignitor red wire MUST be powered by a new non-resistored full 13.5 volts (NOT the factory resistor wire).
The 1847V is the Pertronix I (One). If you still have the stock low resistance coil and this Ignitor, the coil MUST be supplied with by the resistor wire (and a separate, minimum 16 AWG non-resistor wire to power the Ignitor). But if the coil is now a 3 ohm device, then both the coil and Ignitor MUST be supplied with a non-resistor wire. And leaving the original resistor wire in place and connected is fine.
If you have the 91847V, the Pertronix II (Two), then whichever coil you have (preferably a low resistance device), should be supplied with a new non-resistored wire. There is no reason to run separate wires for the coil and Pertronix. And the old resistor wire can be left connected, or disconnected, it doesn't matter.