As far as I understood it, the air mixture screw, for most carbs, determines the mix between air and fuel. Usually used to adjust that mix for low idle conditions. Also, speaking out of turn here, because I ride a 550, but turning out the screw allows more air in, not less gas out the stack. Also, I should have mentioned that it could be a float getting stuck, not just incorrect height.
The Stacks are no different from any other air filter system, in terms of them NOT regularly seeing gas flow. It stands to reason that since it offers less restricted air flow, that the pull through them would slightly help prevent gas flowing the wrong way, not make it worse. This is just an assumption, and not scientific of course. Then again, maybe there is some weird rearward suction from stacks I don't know about...
Either way, it really does seem that the carbs need to come off. Something is preventing the gas from flowing in the opposite direction of you stack/air filter, or allowing too much gas to pool up in there to be healthy. maybe post a question in the performance section where more people tend to run stacks?
Hoping a pro chimes in here any minute...