It might be worth the trouble to take the hub apart again and remove the freehub body. Most I've seen have a very thin washer between the freehub body and the hub shell. If this washer is missing, that might contribute to the mis-alignment.
Another fix would be to reorient the freehub body on the shell, say 90° ot 180° from it's current position as that may reduce or eliminate the wobble.