Do we know how factions for the final round are chosen? The rest of the tourney is blind to factions, right? So do the finalists figure out what to play amongst themselves (and if so, what happens if both only play/collect one faction, like myself)?

My guess is that it will work like the Kessel Run did: the top seed chooses his or her faction.

If you own and play only one faction... I'll avoid my most cynical answer, and instead suggest you get as much practice as possible this week with the other side, figure out a championship list for your weak faction, and borrow enough ships from a friend to round out that list.

Do we know how factions for the final round are chosen? The rest of the tourney is blind to factions, right? So do the finalists figure out what to play amongst themselves (and if so, what happens if both only play/collect one faction, like myself)?

Remember that the tournament rules require each player to bring the contents of one Core Set. You should be able to make a 100 point list for either faction with just the Core set and the two Wave 4 ships. It won't be the best list, but by the rules, everyone will be coming with the bare minimum to play either faction in the final round.