Weird idea coming: Put some long leads on a multimeter while you are driving around and put the leads on different locations to try and isolate the problem.
It could be a fuel related problem, you can try a marine gas tank and an electric fuel pump to circumvent your current fuel system and see if that is the cause.
Can you revert to the old ignition and see if it is still a problem, or was the pertronix a one way fix?
Check your ground, verify you have plenty big wires for the voltage of your car. 6V systems require bigger wire than 12V.
Tighten everything like bigkev mentioned, and there is such a thing as electrical grease (dielectric) that helps reduce water in connections.
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