i have had one problem like this before on this model and it was the foam above the airbox that is stuck to the fuel tank coming away from the fuel tank and getting sucked into the airfilter,it makes thye bike run very rich because of the lack of air flow and causes backifiring due to fouling the plugs with carbon deposits.if it is loose just pull it all of its only for sound deadening anyway.i would expect the rough running low down to be the carbs out of balance or the bike not running on both cylinders
adam bike doctor, October 2006
