I purchased a boat recently that has this engine... I first encountered broken wires on the wiring harness because the previous owner installed new throttle and shift cables and improperly put the boot that holds the wires in place on wrong and it eventually broke 3 of the wires from trimming the engine up and down. I have seafoamed the engine with .75 gallons of gas, 2 oz of oil and 16 oz of seafoam with no results of clearing up the sneezing and hesitation. The engine runs great after a initial hesitation all the way up to WOT. The engine will idle for 3-5 minutes and then shut off with a sneeze every so often. I can crank the engine right back up and it will run another 3-5 minutes with a sneeze every so often. I drained all the fuel from all bowls on carbs along with spraying deep creep through "all" the jets making sure they are free. They are all clear. I have also taken the the 3 fuel pumps apart and deep creeped them also. There has been no crud just clean fuel in all carbs and pumps. Even the screen filter at the motor is clean along with the fuel water seperator that is a racor. Does this sound like a fuel pump issue? Could this be a wire harness issue with a damaged wire..... I did cut 9 wires (all but the big black wire...not sure what that one is for in the 10 pin harness) and reconnected with heat shrink connectors to assure a proper connection and not have any doubts about damaged wires. Sorry for the long post just trying to cover all basis.
Thanks for your Replys
Mark

The carbs need to be removed and cleaned throughly.

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Yamaha Outboard Parts