Chandler, you only need three things for fire; air, fuel and spark.
If you are confident that your valves work as they should and that Pertronix is delivering the way it should, that only leaves one possibility... your carburetor.
Carbs are not built equal. They depend on air velocity to suck gasoline into the ventures with a concentration of 14.7:1 air to fuel. Some carbs only dribble gas in.
New cars atomize gasoline under fifty psi, easily mixing gas with air. Carbs have a difficult time doing just that. Check your carb, since the problem was there before your rebuild. - Dave