Had the same thing happen to my 200 hpdi last summer kept running it for a few weeks it kept getting worst and worst till eventually it wouldn't stay on plane. During this time we tried everything u can imagine to try and figure it out. Ended up bringing it to Yamaha in crowely the screens in the pump and all of the fuel rail and fuel pump had to be taken apart and cleaned if I remember right it cost me around 500 dollars
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