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If you haven't drained the float bowl after using it for a week or so, it is likely there is debris in the low speed circuit. Sounds like you have covered everything else, hoses, filter, etc. Unless there is a lot of debris in the tank, it is probably forming in the float bowl when the gas evaporates.I need help diagnosing problems with my 1999 Yamaha T9.9 outboard. There have been different issues and problems through the summer. Here's a summary of the current symptom (a list of actions previously taken follows at the bottom).
1) engine has trouble starting and won't run at idle speed. If I try to start the engine, it will try to start but won't turn over. I can see the starter motor engage, the water cooling pump is working as the tell-tale is visible. If I spray carb fluid directly into the air intake it will start and run briefly but then die/stall.
2) if I manually engage the throttle link connector at the carb to full throttle it will start right up.
3) if I release the throttle link connector and let the speed drop to idle, the engine will stall/stop almost immediately
4) with the engine in neutral, if I set the remote throttle control to medium/high speed, the engine will start and continue to run (no need to touch the throttle link on the carb). I have not tried to put the engine "in gear".
5) if I lower the remote throttle control - but not even all the way back to idle - then the engine will stall/die
5a) as the engine starts to stall/die when I lower the throttle, if I increase the throttle right away, the engine will continue running at high throttle.
I've had similar symptoms through the summer, with the engine not turning over and starting. It sounded like it wasn't getting fuel. I have taken the following steps already and still have the set of symptoms listed above
a) replaced fuel line and pump bulb from external fuel tank
b) replaced fuel in gas tank, fuel line, engine fuel hosing with new gas with added stabilizer and dry gas
c) replaced fuel filter
d) earlier in the summer, when I was having problems, I took the engine to a dealer/marina and they rebuilt the carburetor. After that, it started smoothly the first time I used it. But after being out of town for two weeks, these symptoms started up again
Time for another carb cleaning, then suggest you drain the carb, small screw on the bottom of the bowl, after using the motor, unless you are going to run it again in a few days.