I'd recommend returning to baseline settings, both throttle plate (synch) and mixture.
The LH carb is the "master", the synch screw actually adjusts the throttle plate of the RH carb only.
You may have noticed the carb synch screw factory painted yellow....their way of "sealing" the screw from rotation. The factory perfectly matches the plates, the pilot screws are commonly widely mismatched. I think Keihin uses a billion dollar flow machine before the carbs ever reach the bike.
Pulling the carbs, and visually matching the throttle plate openings reestablishes the baseline on synch.
A baseline for the pilot screws is 2.5 turns from lightly seated.
With these baselines met, the bike should readily start, idle and accept throttle, provided the circuits are, in fact clear and the fuel levels have been set.
This also assuming the other tuning parameters on the bike are ok (spark plugs, air filter, battery, etc etc.
If the pilot screws are not affecting RPM at all...the offending pilot circuit is clogged or other issues are present. The tiny pilot orings are important little buggers to renew, as well.
Did you actually disassemble and rebuild your carbs? Were the fuel levels set?