I can't help you with the pertronix (no experience there), but since there's a new muffler in the equation, I'd look there. It may not be allowing the engine to "exhale" as well as it needs to be. (Me thinking out loud here, and only speculating:)You may have to reset everything to allow for the changes in the exhaust gas release. Again- that is me speculating, but it does make sense.
I did have a mouse house in my exhaust pipe once. It caused a little more than a sputter, though. Hopefully, somebody will come along soon & give you some pro tips on where to look.
Brad
