I have 2 save states as well as a normal save file. One of them will most likely work although I would have to try it again. I can also probably do things to make them work and get the ship back if you know what I'm saying?
I've only really got stuck in one other part which that one dungeon where you get the Thunder Sword as you have to step on these switches to make a hidden passageway appear that you can't even see after beating the boss.
Actually thinking about I already went to that Moon Tower already. I vaguely remember after meeting that old guy on the top floor it said something about that the moon would shine on some part in the lake. It literal said like lake and kanji for down/lower or whatever it is. I'm pretty sure it refering to that little bit of the lake in the underworld that isn't Magma. I might of very well missed something in the tower for all I know, maybe there's a switch or something you need to press, or I missed something?