I know that the carb boots that run from airbox to carbs are able to be clocked, so that they are straight with the carbs. Maybe yours aren't clocked in the right positions, causing a problem, just a thought. When you go to put your airbox back on, make sure that the boots connected to the airbox have a straight shot on to the carbs, if not, loosen the clamps that hold the boots to the airbox and twist them where they need to be. Once you have everything lined up perfectly, push the whole assembly on to the carb rack and tighten the clamps, you may have to use your right hand to hold the airbox/boots where they need to be while tightening the clamps with your free hand. I don't know if this is your problem or not, just trying to help you out.