Okay, when down in her lair and there's that one room off to the top right, there's an empty container that if you click around it, says its some form of miniature ship.

I'm wondering what this is for? I can't figure out what to put in it, but there were a few chests I was unable to open, is there some item I'm missing?

Nope, the ship model does have a function, which'll be revealed later on in the game ....
What its for is below [img]smile.gif[/img]
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Its Bodhi's ornated coffin, you will need to stake her there, once you've killed her. In it you will find the "Rhyn Lanthorn".
(you get it as a trigger, its in your inventory as soon as you stake her)