If he changed the muffler to a type other than stock, the jets are simply wrong, because the back pressure is different.
Pods change the vacuum level in the carb throat. And that pressure determines how much fuel is drawn through the metering orifices. Orifices need to change diameter to accommodate the different vacuum levels so they can deliver the same fuel quantity as before.
Syncing the carbs involves raising or lowering the slides so they all draw the same vacuum. It is not a mixture screw. On the side of the carb is a pilot or idle circuit air bleed adjuster. This sets idle mixture, as well as how the engine responds to throttle twist.
I recommend you download the Honda shop manual. It outlines what adjustments can be made to the carburetors.
But, it does assume the bike is in stock configuration.