Oh and here I thought anyone was gonna play anyone. Which would make things so much simpler. Don't pair people up based on wins, that is pointless anyway, just pair people up randomly, the number of wins a person has will not affect the outcome of their match, since all decks are already made and cannot be changed, even if someone can see a persons deck before they play them, its not like they can set up a counter deck. Problem solved.
Refer to my first post to resolve the other issue.
This doesn't need to be more complicated than what you people are making it out to be.
16 people per alignment and to go through all 6 marks you will need to win 6 games with each mark, or 5, i forget how that part works, and not checking right now because that is unimportant. I'll assume 6 for the sake of my post. So a player needs to win with each of the 6 marks of their alignment. Who they play is irrelevant, and since there are 16 players, (subs used where needed), no one will be without a person to play against. No one is eliminated based on what I've read, so to go random selection is the only option, and rerandomize if needed to make sure people don't play each other twice, which isn't an issue being there are 16 players.
-edit-
if you dont know your way with the game very well, this isnt the type of pvp event you should participate in. your deck can become unusable if you do something stupid and you only have yourself to blame.