I had nothing but problems with my Petronix, they last a couple years then go bad, either magnets came out or unit burnt up leaving me stranded on each occasion. Switched to MSD distributor and ignition box and never looked back. Sounds like you have an intermittent short somewhere in your ignition, either coil wire, ignition switch, or bad spark plug wire perhaps?
I think you need to use suppressor wires for the Pertronix I-3 setup. The RF interference from normal solid-core wires can affect the other systems under the hood. I put in a 7mm suppressor set when I switched over to the I-3 on my 67, and I've had zero ignition problems for the last 5 years. The older Pertronix units with the wheel were not reliable, but I've had good results with the I-3 since I installed it.
I had nothing but trouble with the pertronix III. It idled weird and intermittently ran bad. I put a clear distributor cap on and saw the spark was all over the place . We changed it out and problem gone. pertronix kept telling me I grounded it wrong. I like their old products
The petronix site implies that the Flame thrower 3 coil should be used with the 0.32 Ohms. Might be the problem....
I am using a Flamethrower III coil on this car..and I still have the same issue. I am also using NAPA Belden wires, they seem to be pretty good too. I did try swapping the Pertronix Module, so Im on the 2nd one with no changes. the clear cap thing is a great idea, I ordered one to see just whats going on in there.