Hi Matt,
Problem with using any pointing precision programs (Tpoint etc) rely on repeatable goto accuracies. It can take gear errors, angles and eccentricities into account, but they are all absolute, and never really change.
Mirror flop is different, as the mirror may not always slip/slop/flop along the baffle tube or its mirror support the same amount every time, so its relative to the last position it was "Sync'd". For this reason your accuracy will never be excellent. An easy test is to setup your CCD camera and image a bright star low on the horizon, then slew the scope to the Zenith (Up) and slew back to the same star using goto, numerous times and see if it centres you star within the ccd sensor by stacking the images together using Overlay or Sum.
What you should see will be similar looking image like a bullseye in a shooting range, where the star images are tightly grouped. This may give you a best fit value to use in your calculation for high precision.
Theo
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