Tried new plugs yet? NGK is the only way! After that, I'd be looking at the valve adjustment and maybe try running a compression test or both.
You could also try a little de-carbonizing exercise by making sure both cylinders are firing good and setting the throttle at around 2,000 rpm. Then just take a plastic squirt bottle of tap water and slowly, judiciously "mist" a pint of water through the intake. That is a very effective way to clean up the combustion chambers and the tops of the pistons. Then you can keep it clean by running Sea-Foam or Lucas fuel injector cleaner in every fuel load.
Good luck.