Not sure you have to tear things apart. If the horizontal stab is aligned properly as you say, But the vertical is off center by a 1/4", it may fly okay as is. (So long as the vertical is in line with the centerline of the fuse.)

Can you post a couple pics, like from directly above, and from the rear?

I think whether or not you tear it apart will depend on the type of plane, and your "vested interest" in it. It may fly fine even if it looks a bit odd.
Dennis-