Is it both cylinders or just one? I had one that misfired on the right cylinder only even when i switched the plug wires around. The culprit was a crack on the inside of the flywheel near the hub part not on the magnet. I would yank that off really quick before you mess with your carbs. If you switch the plug wires around and it backfires in the opposite cylinder you MIGHT have a problem with your coil or one of the blocks on your flywheel. Your pulse coil could be out of adjustment too. Just some info to get you pointed in the right direction.
Give us some more info on your setup. Any recent mods you did and whether you have a timing plate or not.