Not usually.
The only stock air box mod that has been proven to help at all is shimming the Y up a bit.
\With stock exhaust (or slip-ons) the stock air box with 150 (or possibly 147.5) Mikuni Main Jets can help though.
My 2000is stock jetted with Supertrapps and my brothers friend removed the Y and then replaced it but with holes drilled in it and it ran wore than when stock.
I run it now with the stock air box, a K&N filter and stock jets and it runs slightly rich but did 118-119 RWHP on 3 different dyno's.
I plan on installing 150 mains to lean it out a tad.