You have a lot of joke mods, which could do all kinds of things.
It might be best to disable the second half of your mods, load and see if the problem persists, then switch to the other half to see if that has the problem. Then, once you’ve figured out which half has the problem, divide that in half, test again, and so on. Best strategy for this kind of weird bug.
Is the clone spawning as you talk to the captain? Is it after a dialogue line? What’s the immediate trigger for the clone?
For Morrowind Unleveled - you don’t need to run both:
Morrowind Unleveled 1.1-522993/MorrowindUnleveled.ESP Morrowind Unleveled 1.1-522993/MorrowindUnleveledVanilla.ESP
I don’t think I saw a bashed list in there? Maybe OpenMW does magic staff with leveled lists, but I feel like you have some stuff in that load list that’s cancelling out other stuff. Have you run your list through a tool like LOOT?