I found the best way to remove the ship is:
1) Remove the sails from the ship (4 screws) and set aside.
2) Go into the ship test menu and lower the ship into the "sunk" position.
3) Eject all the balls or plug the trough with a towel.
4) Turn off the machine.
5) Lift the playfield into the upright position, leaning against the backbox.
6) Disconnect the 4 electrical connectors (motor, switches, 2 solenoid)
7) Remove the bolts connecting the ship mechanism to the bottom of the PF
8) Pull the ship mechanism away from the PF.
Easily comes out through the hole in the PF if you remove the sails first. You can get it out with the sails connected, its just a little more tricky.