I recently picked up a 2006 G3 1860 with a Yammie 90hp 3cyl-2stroke.
The motor starts and runs well. It seems to idle OK, as smooth as a 2stroke/3 cyl should. I know it's not going to be super smooth. During idle, the motor will sometimes "cough". Sometimes it will cough once or twice and keep running. Then it will cough again, dies and will start right up when I bump the switch and will idle for a while before it coughs again. I had idle adjusted and the carbs synced and compression checked and everything there is fine. I dumped all of the old gas that was in the tank when I bought it and have started over with fresh gas and all of the additives. I'm using SeaFoam and it does seem to be smoothing out a little better than when I first got it. I also added a Racor water separator. The service manager at the dealership that did the work said what was left was to "go through" the carbs, cost $600-700. I don't want to spend that kind of green right now. Another mechanic that I talked to at my marina told me that this is characteristic for the 2 stroke Yamahas and not to worry about it. Is this normal for this motor? What should I expect from this motor. As far as running rpm, 4000 seems to be the sweet spot and it runs like a champ. Opinions?

Sounds like the carbs are dirty and you can burn the motor up if you keep running it like that. That is not a charecteristic of that motor it should idle fairly smooth with no coughing that is called a lean sneeze.

Could be as simple as the idle air adjustment. I see alot of Yamys with the idle screws out too far. Try srewing them in 1/2 turn.

Sneezing is not a characteristic of that motor. By sneezing it is telling you that it is too lean. On the Japanees motors when you screw the air/fuel mixture screw in, you are enriching the motor. Screwing it out leans it. If you take the air box off the front of the carbs, start the engine, allow it to idle. You will see which carb is lean, It will chirp and possiblely blow fuel out the front of the carb and almost immediately suck it back in.
The air/fuel mixture screws on Yammmy's regulate the amount of air which inturns produces vaccuum for the fuel. Less air-more fuel, More air-less fuel.

I have an 06 50hp and is sneezing also in the schematic the pilot screw is behind a brass plug. Do I need to remove this plug.

Problem I have seen is the mechanic will set the idle air with motor not in gear. Also make shure the bowl vent is clear.