As far as I know the jet kits are designed for the stock air box and not for pod filters.
Although a carb is a carb and a jet kit is a jet kit, I know my bike runs like crap when I remove the air filter as it doesn't have the proper back pressure. It bogs out when the throttle is used.
I think the extra washers were for the slight difference in the intake runner lengths for the outer carbs being slightly longer than the two inner carbs.
As your bike has pod filters on it I can't really be of any more guidance, sorry.