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I would just have the CCD in the scope, slew to a 'busy' field - like into the middle of the Milky Way, and start PHD2 looping - now rack the focuser of the guide scope until the stars are focused on screen.
I don't know about the 'slightly out of focus' mantra.... just lock PHD onto a non-saturated star.
To do the eyepiece switcheroo you would first need to ascertain where the EP and CCD are parfocal....
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