Simon,
I'm glad you are making some progress with your mount!
I've never heard of using PEMPro to measure error in declination. Might you explain what you have done here? Since the declination axis typically doesn't move, except for guiding corrections, how can there be meaningful PE? Sure, if the axis were always rotating it would matter, but that isn't the case.
I personally wouldn't have any concerns about T-Point not agreeing with PREMPro's drift alignment. You wouldn't actually expect them to agree! T-Point is taking all sorts of things into account such as refraction, and specific mechanical issues with the OTA and mount that can be modeled. I have found T-Point to be somewhat sensitive to polar alignment wrt where and how many points are collected. I have obtained best results only when the points are spread equally on both sides of the meridian. I have been told specifically that this should not matter very much but my experience has been otherwise.
Peter
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