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I have a serious issue with my 2003 Yamaha 115. The engine is an inline 4 cylinder with fuel injection. 106 hours.

Last fall I noticed it ran a bit "rough" at ~1900 rpm. It would disappear slightly below or above that RPM.
No other issues last year.

Prior to running it this year I changed the plugs, new fuel-water seperator and engine fuel filter. Running on internal tank full of fuel stabilized gas from last fall. On my season shakedown cruise 2 days ago, started fine, idled fine. Slowly warmed up, got on a plane, cruised at 32-3400 with out issue. After 10 minutes of running I stopped at an island dock for 5 minutes, engine idling.

After leaving the dock and slowly accelerating, it started to "bog down". I could not get on a plane and the engine sounded off, not smooth, like it was not running on all cylinders". In neutral, at 1300 rpm, you could hear it run rough. In gear, with full throttle the engine would not go above 2500. At one point giving it more throttle, it did smooth out for a few seconds, accelerate, then ran rough again. I limped home at low speed. I double checked spark plugs and wires are tight/good connection.

I was thinking of eliminating fuel as an issue by running it on a separate tank of clean gas prior to making the dreaded call to the dealer on Monday.

While I have a shop manual, my skill level on engines is basic. Can change plugs/fluids/fuses.

Any suggestions?