If you're still using the Yamaha oil injection system, then it sounds like you are getting oil, but not gas. I had the same problem with my '99 115 Yamaha. If I could baby it enough to get it past idle speed, it ran great at wide open throttle. But keeping it running at idle and having to hit the choke a few times to get it to throttle up, was very frustrating. once the motor is running past idle, the fuel pump on the motor is sufficient to get the fuel from the tank to the motor. I accidentally figured my problem out by replacing all the fuel lines. I ran out of fuel line hose and the last section from the primer bulb to the motor, I used a piece of clear hose. when trying to keep the motor idling long enough to get out of a no wake zone, I looked back at the motor and saw that that section of fuel hose was full of large bubbles. It had more air that fuel in it. Once I got it to throttle up, it was full of gas. I replaced my primer bulb and it's fine now. When you take the plugs out, see if you smell gas on them. I bet it's just mostly 2 cycle oil. Hope this helps.
