Okay not knowing for sure what is going on with the holes not lining up. About all we can do is check things and see if something is put together wrong or something is wrong with the detector parts.
You have a 3 piece shaft, the one with the control box, the center section and the one with coil.
Turn the detector up side down and take a eye shot down the bottom of the shafts and see where the holes seem to be off center, that will tell you where the problem is. Remember you have one snap hole in the control box shaft, make sure your center section snaps into the control box section.
After you look and check things over at some point you will either find that you have something put together wrong. If it turns out that it is a part problem you need contact FT and see what they will do, I am sure they will make it right.
Good luck,
Ron in WV