Fun, ain't it!
1. Turn the motor upside down.
2. Look up the hole where the shifter shaft goes--is it centered? If not...
3. Bend up a coat hanger and push it back on center from an opening about 4 inches above the cavitation plate.
4. Ease the LU home, being careful to align the water tube inside that plastic extension tube.
5. If the shifter shafts don't want to go together, do NOT force them! They only go one way (there's an 'orphan' spline there). If jammed together you might yank the shifter shaft out of the LU getting it apart again. Yikes!
Be sure both ends are in neutral, and that all slack is taken out of the shifter shaft at the LU (CCW as I recall).
Good luck!
Jeff