Your comment "when I pull the plug wire off on the clutch side still runs but if I pull the plug wire off the mag side with the plug wire back on the clutch side the motor quits" tells me that the idle is probably not adjusted properly. Start by adjusting the throttle cables then sync the carbs. Also check the choke cable adjustment and pull the choke plungers to make sure the rubber on the bottom of the barrels are in good shape.
These motors are a little finicky. Everything must be tuned and adjusted properly or you will get the dreaded "Kawasaki bog". Which, from your description, you have the bog!