One thing to check with your Pertronix is the "rotor phasing". Best to install an old distributor cap with a hole cut out to view the rotor tip with a timing light. You should see the tip near the post, varying only +/-15 deg due to vacuum advance. If not, it could be sparking to the wrong post at times. I recall reading that this is sometimes a problem with Pertronix. The Holley XR700 manual (latest) explains, which you can find in a web search, plus several posts here. Also, SlantSixDan found many poorly manufactured slant six caps out there, which you can read about here or on slantsix.org.