why don't you just duplicate the references and delete the originals? everything would reset if you disable your mod...
I suppose. I've never thought of that. It certainly should work. At least for the statics.
Hmmm . . . But there are doors connecting to the ships interiors. And the interiors are related with vanilla quests. I could replace the doors and link them to the interiors, but I am not sure I would not break something in the game.
this can easily be solved: change the collision in the nif to animated and it will move. take a look at the oblivion elevators to see how it is done.
i also did that for my sailing mod and it works perfectly for doors, containers and furniture too...

Yes, I know.
I've been using the ARGate01 as a flying platform for almost two years and it does not have the problem. I mentioned it to JDFan a few months ago and he looked into the mesh and figured it out. I must mention that I have no modeling knowledge (although I can enter nifscope and do thing following very detailed instructions. lol).
so, what math are you looking for? sorry, i did not read all the posts... as far as i understand you need to move object in 3-dimensional spaces? should be no problem with trigonometry... if you explained it somewhere please link me there. maybe i'm thinking about the very same thing. i want to rock moving ships... this is fun.

The only piece of math that I still would like to have is how to calculate the angles of an objects so it keeps the same orientation with a moving 'anchor'.
I have the math to position and angle any object on the deck, relative to the ship, as the ship moves and tilts along any axis (this is used in this mod). But only if said objects are, originally, at zero X and Y angles.
If an object is initially tilted in either X or Y angles, I need the math to recalculate its angles, so they stay in the same orientation relative to the ship, as the ship rocks.
Easier to explain with an example: I can make a stand up barrel stay (visually) in the same spot on the deck, but I don't have the math if the barrel is initially on its side. I can still position it at the right spot, but not angle it correctly. Fortunately there are not many of those.
Rocking a moving ship should be no different that rocking a static one. I developed a function to position an object according to the ship present position and orientation. It really does not matter if the 'anchor' object (I use the hull as the anchor) is in the same place as in the previous frame or not.
So you only have to deal with moving and tilting the hull. Everything else will follow along.
Feel free to use anything from my mod, that you still don't have.
You may have to tweak the rocking algorithm as, I suppose, moving ships will rock more back and forth than sideways.
It would be cool if moving ships banked to the sides as they make curves in the water.
I considered doing that on my Sail Away mod, but I won't go back to that project any time soon.
And, since you are here, congratulations for you sailing mod release. Looks cool.