it's really very simple - i've probably done more of this than practically anyone... don't worry about anything else lining up. Just get yourself in the center (as you see it), set your bubble levels so your standards are vertical, ideally locate a reflection of your camera in a front window and center it -(but eyeballing it works too) and then set your vertical shift. Worrying about anything else is just asking for a migraine. it will take care of itself.
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