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Shoot object first, and then take flats, so you'll be in focus.
I don't think there's any point in taking flats before you begin, unless you have an observatory and nothing ever moves. Consider that you may need to rotate your camera (yuck) to frame your object (more yuck).
+1 for being a stickler with keeping camera always perfectly oriented east-west or north-south.
Regards,
Humayun
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