Join Date: Feb 2011
Location: San Francisco Bay area
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Re: Yamaha 9.9 High Thrust Shifting Problem
Before you start rebuilding the gearbox, I suggest eliminating some of the simple (and inexpensive) things that could be causing the issue.
The first and most obvious would be a misadjusted shift mechanism. I had precisely the symptoms you describe on my Yamaha 8, when the shift rod was not properly adjusted.
The second would be an issue with the reverse shift / tilt interlock adjustment.
Bristol 31.1, San Francisco Bay