Thanks for your help on this, I'll give it a shot - it's worth a try, I'll test by adjusting throw and manual shifting to try and narrow down the possibilities.
I do have a feeling though that the servo is failing. With the system powered on, I tried forcing the shift servo to a different position with my finger, and it doesn't return to its original spot. Maybe I'm wrong, but normally it's supposed to return to its programmed position when running, right? I will be ordering a new servo just for good measure and go ahead with the swap anyway, it's the easier option than a full teardown of the gearbox but at least it will provide a surefire way of diagnosing the problem.
Cheers.