[X] Captain: Luffy
[X] Administrator: Taylor
[X] Second: Nami
[X] Third: Zoro
It doesn't really matter if Luffy's captain or not. He'll still be making the majority of non-tactical non-strategic decisions. Might as well let him keep the title and the diplomatic/reputational weight it carries, and let the person who knows how inter-gang—sorry 'inter-pirate'—relations do the hard work.
Also, I trust Nami's greed, empathy, and sense of direction to make her a better stand in leader than Zoro with his potent shounen and cluelessness. Zoro's a boss character, not a leader of men. It's useful to have him as third though, as an attack leader and intimidation method.
"Why is everyone doing what you say? He's the captain, and they're the second and third."
"I have a particular set of skills, that make me a nightmare for people like—well, actually, just people in general. They had to come up with a new maritime position to fit me."