Nat - I've got an idea that Ted is closing in on the right culprit - this sounds to me like a "lean miss" at idle. Which can be had by over-advance at idle speed.If this engine is timed to spec and has the correct vacuum scheme in place - try raising the primary float level just a hair. Also - you might want to reduce the spark plug gap a bit to say .038 to .040.
The Pertronix will handle a "hot" coil down to the point of 1.5 OHMs minimum resistance. Are you running the Ford coil and ballast resistor?
I'vve been running the Autolite AP46's in mine - have a set of 45's (slightly colder) waiting for the right day to go in next.