Mike, he stated his carb sync is "spot on." As mentioned in the other responses, yes indeed the free flow mufflers can indeed cause unexpected strange things to happen. OK to make an engine "Breathe" more efficiently it is a combination of allowing the air in less restricted, allowing the exhaust gasses to evacuate faster, and to properly jet the carbs. Unfortunately many well intention-ed mods can go haywire if the modifier does not really know what they are doing. The real issue is improper metering in the carbs, or even though they are drawing the same vacuum at idle, the richness of even one carb not being exactly spot on will effect the overall response of the unison at all throttle positions. To properly set the richness you need to monitor each exhaust with a CO analyzer separately.
So, the answer to your issue is not necessarily an easy one...