I had a similar problem on a newer (2001) Yamaha. Had to replace the prime start (choke) module. Still has the hard start problem sometimes. I found if I pull the carb float bowl plugs and pump the fuel line bulb to clear out the carbs it will start (PITA).
Not sure about your choke system, on mine I have to push the key in to prime. I found that if I cracked the throttle before cranking it would crap out everytime. Try starting without cracking the throttle.