Ooooh, I must get back to reading this now that I have time.

I think I'm behind a few chapters...
Anyway the Scarlet and Vin Relationship - I don't know if I'm such a big fan of forcing them into casual conversations - it would slow down the story and may feel out of character. Instead, focus on moments within the action to build them up and show more character. Find what each one will eventually admire or like about the other, and have moments where they show that side. If one admires nobility, or loyalty, or cleverness, or thoughtfulness have a scene where the other shows that side of them self. It can be slow and gradual - evolving from dislike, into appreciation, and from there into admiration or affection.
Also, force them to work together. Put them in a situation where they have to depend on each other to advance the plot. I know it's been done to death in films and stories, but there's a very good reason why, and that is because it works. Take two characters who hate each other - force them to work together to reach a common goal - throw in those moments where the characters realize something they appreciate about the other (or maybe they discover something about themselves) - and bam! A tried and true friendship and/or romance. That's not how the real world usually works, but it works in stories, because stories are all about changes from one state to another. But if you try to force them to bond it'll come off as forced. Let it happen naturally; look for places those little moments could be while you're writing. As those moments build up, and they come to truly appreciate one another, there'll be more excuse for them to spend more time together and get those bonding moments, where you can show even more character.
I also like Vin's name as it is. XP And I think you should just go with El Dorado - I mean why not? If you're gonna be a pirate, you might as well go all out, right? I mean yeah, practically speaking what are you going to do with a City of Gold? Not much you can do with that. At the same time it's a
City of freakin' Gold. I mean, who wouldn't go after something like that, even just to see if it
exists? XD But you know, it doesn't matter what the MacGuffin is - it could just be something of sentimental value even.
Also - thumbs up to more of Scarlet's past. ^^
Last piece of advice: don't bother fixing anything you've already written until the whole rough draft is done. Why? Because how you think the story will go, and what the story will end up being are too different things. You may discover upon finishing the rough draft that you don't need something you added, or you may need something you took away. Be flexible and make notes, but hold off any major edits until you have a finished draft to work with. ^^ Once everything's written you can switch things up, add and subtract this or that, change what ever you like. But if you start editing you may never stop. XP