Even if the Petronix unit is a problem for some people (not for me), it clearly is not the cause of your problem (which was observed before you put on the Pertonix unit).
One "fix" for a Pertronix problem is poorly grounded distributor. You might want to run a ground wire from a distributor-cap-clip screw to the head (to a bolt/screw that holds the coil to the head).
