Seems to me, now that you have less restrictive exhaust the "air pump" that is the engine is flowing more CFMs per given period of time increasing its volumetric efficiency. With no change in carburetion this would result in a lean mixture which could definitely give you a miss.
Try richening the mixture from the usual (GAV, larger jet).
Take a look:
http://mechdb.com/index.php/Exhaust_back_pressure_myth