There is a whole lot to your post, but I will focus on the well and mist spirit for a moment. There are two pulses she feels, one from the mist spirit, and one from the well. She recognizes the pulses from the mist spirit, but the well is a mystery to her at first. The fact that the well's pulse gets stronger fits with Kwaan's writings about the Millenial Power. As the well got stronger, so did the pulses. It is interesting that she begins to feel it in book 1, if only for a moment. It eventually becomes strong enough for her to feel it through her Hemalurgy earring, which she can enhance through Allomancy. I am completely convinced that her ability to pierce copper clouds is due to the combined powers of Allomancy and Hemalurgy. Alendi had piercings but no Allomancy, and he could feel the pulses as well.
Now for the mist spirit. The mist spirit didn't want to keep Vin from the well, but rather wanted to keep her from giving away the power. Therefore, It was trying to remove influences that would prevent her from keeping the power for herself. If the mist spirit didn't want her to find the well, it could have simply killed her. Instead, it tried to take her earring from her ear, tried twice to hurt Elend (and succeeded the second time) so she would use the power to heal him, and it also tried to keep Elend from Luthadel so he wouldn't influence her decision. Finally, I believe it was the mist spirit who was tearing the pages of the manuscript. It wanted them to focus on that sentence. Ruin had already changed it, and would have wanted them to move away from it, so they wouldn't question it. The mist spirit is definitely linked to Preservation somehow, I just can't say to what degree.