It may be that the later model is different, but my understanding of the tank on the '98 version at least is that there are three pipes attached to it. There is the fuel outlet to the carbs via fuel filter/pump and two others, one of which drains the rainwater from around the filler, the other connects via the filler cap and is the breather. The drain and breather connect to two rubber tubes that are routed down behind the engine to the outside world (I think more recent models use a funnel rather than directly connecting to the tank). So, even if you do overfill the tank, I can't see how fuel can end up on the air filter rather than the ground.
The crankcase and carb breathers do terminate in the airbox. Is it possible that, rather than anything to do with the tank, you've a problem with a stuck float?