make sure the NUT is centered first. Assuming the high-E is off by the upper fretboard... there is often some play in the pocket where it can torque causing this. I would first try to loosen the
neck screws (4) a half-turn or so. looking at the
neck joint (rear body) you will move the neck so to eliminate the problem, then retighten the screws. If the pocket is cut right and stable, it should hold.
ALternately you could stand the body on edge (lower horn to body) and use leverage to position the neck as you tighten it. It is easier than it sounds here. Anyways try that before redrilling. It is a rarity the neck/body is drilled wrong... glen