Odd shifter problem, need advice

Uncle Bob said

I was hoping someone would just say make the shift rod a turn longer (or shorter) but apparently it's not that simple.

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You can certainly try that. The issue of the shifter gate not lining up comes into play when you go too far.
Try to lengthen it one, possibly two, revolutions off center and see if the shifter will allow it.
Shouldn't have to do with clutch release though.