Did you check the rotor button height?
I had a hell of a time installing pertronix in my mustang. It looked fine, but consistently failed to fire on several cylinders. It took me a couple frustrating weeks to figure it out. Turns out they can be sensitive to the precise height of the pertronix rotor on the distributor shaft. If magnets in the rotor misalign they fail to fire. In my case, five were fine, but three of the magnets inside the rotor ring must have been at slightly different heights, so they misfired, while others fired.
The solution was placing a garden hose washer under the rotor, which raised all the magnets into alignment.
Runs great now, and I would recommend, except Pertronix instructions and tech support were not helpful about this, though they seemed aware of the problem.
Last edited by wurlitzer46; 11/03/2012 10:18 PM.