The Pertronix has the pick up coil inside the ignition module. No way to reverse wire it unless you cut the module apart. The only wires to the Pertronix are 12v power and coil negative. I don't think you would get any spark at all if you get those reversed. You could have trouble but still sort of run if you have the coil positive and negative backwards.
This sounds like a case of "90% of carburetor problems are the ignition." I would make sure there isn't anything loose and the gap between the Pertronix and the ring of magnets is not too wide. Also check to be sure the rotor makes good contact with the cap, no loose screws, and no issues with wire splices.