Welp, ignore all that. Thanks to a suggestion from n_wolf, old Factions is back. Upgrading Factions did wipe the data though, so you still need to set them up. Enjoy! :)
So the factions plugin has kicked the bukkit. Seeing as it hasn't been updated in over a year, I'm surprised it didn't happen sooner. Your factions have been deleted and will need to be reclaimed.
Luckily a nice developer is working on a new factions plugin :)
Type /f help to check out the commands. Everything should be very familiar, with only a few changes. The best thing I've noticed so far is the private factions chat is wonderful. Just type /f chat faction and only people in your faction will see what you're saying. To return to global, type /f chat global. It's awesome!
If you need any help, go to this thread where we can have discussion about the new plugin. Enjoy!