i think your jetting a little off i ran 330 mains in my 04 with unported cylinders sst pipes dual k&ns and milled head at sea level with 13/40 gearing and 22x11x8 8 paddle haulers no prob pulling all the gears
your going to have to leave the lid on it holds the stock filter in place id just remove the snorkle and drill holes on the sides of the air box and dont forget the proper jetting