You say that the bike isn't running well and that there is oil in the air box. If it were me, I'd do a compression check on both cylinders. Reason being, if you were to have a bad compression ring, head gasket, or valve guide problem (does it tick, tick, tick?) the excessive blow by caused by that problem will manifest itself through the crankcase vent, which in your case is routed into the airbox, thus oil in the airbox. For your sake I hope that it is just overfilled with oil.
Good luck.
Bananas!