It's been a few years since I installed my ST6002 control head
and even longer since I installed the S3 Course Computer, so my memory of the calibration process may not be that accurate.
I think you are saying that you can put the control unit into calibration mode and can see the options to select User and Dealer calibrations. You do not see the Seatrial option. When you go into the Dealer calibration mode you cannot set the vessel type to sailboat.
It does sound like there is a software problem in the course computer. Either that or the ST6002 control head
calibration process has changed. That it might change is possible as Raymarine often updates the software and may or may not update the documentation
to reflect the change.
Either way, course computer software problem or a need for updated documentation
, I would take that back to the Raymarine forum for assistance. They will want to know the model nr of your course computer.
However; I doubt either is a cause of the problem (assuming this was a working AP before you started taking it apart). They may be symptoms. It sounds to me like there is serious problem in the course computer that is causing the hard over drive unit problem. If so, that will only be fixed by sending your course computer to a Raymarine service
rep and the cost of repair may be a significant chunk of the replacement cost.