i'd support the front end, and mount everything in place, with the wheel just touching the ground. the triple mounting bolts should be snug enough to hold eveything in alignment, but loose enough for the tubes to twist in the triples.
stand in front of the bike, hold the front wheel with your knees and twist the triples a bit. you may find everything lines up much better, but check them with a piece of glass against the fork tubes, or other method.