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For accurate polar alignment, Pempro is all you need. Your graphs are indicating hardware issues, and when you have flat sections as you show, you sampling hot pixels. A basic polar alignment in PemPro [to say 0.6 arc minutes of error] should only take 15-25mins [depending on the stability of the atmosphere].
It is a good idea to watch what the star is doing in Maxim like you say, as then you can tell if the drift is too severe for an accurate measurement. Being far off the pole can give you very misleading results too. But I assume you are close as you are revising a previous alignment.
Its important to make a cheat sheet of which way to adjust and for how much per amount of error. Making even marks on your adjustment knobs can be of a big help.
But definitely, you should not get flat spots in your graph when viewing it at 10 arc seconds of drift scale.
Good luck,
Steve
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