and the paper filter restricted the air flow too and acting as a choke
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Do you have any data that confirms your statement? No, you don't and your remark is nonsense. Why would a motorcycle manufacturer want the paper air filter to work as a choke?
When I say "choke" I mean less air and more gas.
If you take the air box and air filter off of the motorcycle it will run leaner.
The idle will slightly increase and the throttle response may not be as good.
Also it may pop on decel after revving it up.
When you put the air filter back on you will notice an improvement in the idle (going down ) and the better throttle response and no more popping on decel.
If you measure the inlet of each carb and figure the sQ. inches if intake, THEN measure the inlet of the air box, you will notice that the opening of the air box is LESS than the area of the 4 carbs intake openings.
So it is just like putting you hand partially over the carb opening, which chokes or richens the mixture by giving them less air and more gas.