only problem you are going to have switching them is you cant hook up the choke tube when ya put the carbs on the wrong sides. also, the pilots and the mains seem alittle high with fmf pipes.
also, the coil fires both plugs every revolution so yeah you can swap the wires side to side. if the problem follows the wire then you have either a bad wire, coil, or plug cap.
are you sure you have the carbs clean and the pilot circuits free of crap? what about the air screws are they set the same on both carbs?