Should there be two, three, or four different plots?
I'm actually planning a game like this, but with Cs pets and items.
I think one direct, long plot would be easiest to handle, with the choices they make directing the outcome of the game. Like if they make a wrong choice, and end up in jail, it could change how people trust them later, and if people are unable to do specific quests or something.
Or even give them an option to go by the plot(s) in a free world environment. Like if people want to go by the plot, let them, but if they want to go track down a bounty hunter and rob them, let them. Of course, within Cs rules.
Should I elect certain kiamaras to play characters rather than roleplaying alongside everyone else? They would be people your kiamaras meet along the way rather than it constantly being NPCs (Non Player Characters)
If you want to use civilian kias, I suggest set up a thread where people willingly volunteer their kias to be these characters. I suggest you put it in writing that you/mods will be controlling them, and that they will not be able to play as actual players in the game.
It will be a bit more work to organize a thread to do this, but it would be a neat way to bring in other's kias instead of having a butt-load of NPCs.