Pilot Air Jet? :? Perhaps "Pilot Screws" - these are a fuel flow control that is in the circuit after the Slow-Jet. As a fuel control, counterclockwise will increase fuel flow richening the overall mix. Almost everyone w2ill advocate properly adjusting your idle mixture on a warmed bike anytime the carbs are serviced. Since you're changing the size of your slow jet, and your carbs have been gone through... Yes, the idle mix should be set to the new operating configuration of your carbs.... does the pilot air jet get leaner as you screw it out ? Does the jet change require a different setting from the original with the #50 jet ?
FWIW, the OEM "Idle Drop" procedure is kinda the normal way to set/reset idle mixture...