I've just been to the smallest room where I do my best thinking and I thought, things can be relative to a datum or relative to each other.
So using gravity as the datum, a level is placed at the headstock end for example and that is brought into alignment with the ground.
Next everything else is brought into the same alignment either by making it relative to the ground or relative to the headstock. I would suggest relative to the headstock being the most accurate in this instance.
The tools required for alignment should therefore be chosen to achieve these requirements.