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I just recently purchased a 1988 17 montauk with a 2001 f100 yamaha 4 stroke. The motor had a complete tune up last month but has began to run terrible. The motor has trouble idling and sputters and dies when given throttle. If I can get the rpms up it seems to run ok other than sometimes bogging. I replaced the fuel and checked the fuel filter. Not sure where to go from here.
I agree, May be water in the fuel. Is the fuel old, perhaps from last season? I would get rid of the fuel in the tank, and add a 10 micron water separator to the system. Yamaha has a product called ring free which can clean your engine. Also another product called Seafoam, available at most auto supply. I use this stuff regularly.
I would run the Seafoam through this. If this a carb'd engine, can they be drained easily? I have done this on 2 strokes when I have had water issues. Water is heavier than gas and it will sit at bottom of the carbs until the engine runs like crap. Eventually it will not run at all when the carbs fill with water.
I would post your question on the Yamaha forum. This site is hosted by boats.net they a very large online Yamaha dealer.
start with fresh fuel, as mentioned above, the "RING FREE" fuel additive is a MUST, and is suggested to be used every time out by "Yamaha" (yes even on 4-strokes), the stuff REALLY works, check the plugs at the end of the season, "Squeeky Clean" ! !
mw