I'll do my best to explain how the auto choke works on your 9.8 Yam.
There isn't a butterfly choke, rather a starter plunger which is controlled by a vacuum valve which senses the temperature of your head. Richer when cold, leaner when warm. After the motor gets warm enough you should see the plunger change position, I can't remember if it drops or rises up. Manual says the thermostat must not be removed because the sensor will think the motor is cold and richen the mixture.
If you look in a factory repair manual the choke system is explained clearly.
Have you tried to monkey around with the pilot screw?
Seat it lightly and back out 3 turns as a starting point.
Sounds like you may be in need of a carb cleaning.
Don't ask why I know these things other than over the years I've gotten to know mine more than I'd like to.
Hope this helps.
Scott