On my b ike, similar (-90) there is a set of vaccum-carbs. This type of carb need the STD-airbox to work. This is because they work in pressure difference, you do not lift the thottle via the cable, it is controlled via (under-) pressure.
Removing airbox messes the pressure differences up, and all kind of problem appears.
If you do not believe me, put the STD-airbox back and test.