It looks like you're making wonderful progress! Remember with your emission bike, and going up to the #40's, you can successfully go up to 2 turns out with the idle mixture screws and fine tune to your area.
On this particular ST forum, it always seems to be a controversial topic about synchronizing the carbs with, or without having all the air filter components installed. It just doesn't need to be... We are measuring VACUUM in the intake manifold, under the throttle plate and venturi. NOT the AIR FLOW above the carbs, or the mixture. Years ago, because of this controversy, I took the time to balance AND do the idle drop on a set of carbs both ways. My results were exactly what I figured. It makes no difference if the stuff is on, or if the stuff is off....The readings were the same. However, it is dammmm near impossible to reset and tune the idle mixture screws with all that crap installed. Especially an emission/ABS bike. So with that being said, nobody here is wrong on which way to balance the carbs. But they're not correct either....
Personally, I leave everything off for ease of access to the synchronization screws and the mixture screws.
Also... You are setting/balancing the throttle plates for the smoothest and strongest IDLE speed. Thats it... The vacuum readings per cylinder, will always change as rpm changes. This is normal. Over the years, some guys have set their carbs at say, 3500-4000 rpm in hopes to get the smoothest, most vibration free ride while touring. But the idle sounds like absolute garbage and is weak. It's best to set at idle.
