First step is to do a manual realignment as close as you can get it. Do this one global axis at a time. View from the the side and rotate until it looks right (right being parallel with the Y axis and perpendicular to the Z). Repeat for front and top view. Using these views automatically constrains rotation to the axis parallel to the line down which you are looking to the target. Side constrains rotation to X, Front to Y, and Top to Z.
I take it you have a mirror modifier applied to that mesh, yes? If so, take the mirror modifier, turn on 'clipping', pull the mesh away from the axis of symmetry, drop it, grab it again and pull it together until the central ring of vertices meets its twin. They will automatically merge.
If you haven't used a mirror modifier, select the central ring, and press S-X-0. This scales along the sideways axis by 0, making all vertices share the same X coordinate. Press N to bring up the transform properties menu, and set X-Pos to 0.
If this fails, upload to mediafire and PM me a link. I will do it for you.