What story cards should we be using for Regionals? The tourney rules say the cards from Shifting Sands are legal for the 2013 tourney season. Is that still the case for 2014?

Also, what ever the Story deck consists of, is it OK to use proxies for that if we don't own the pack?

Yes, The Shifting Sands story deck is still the official one, and is required for Regionals.

The official line is that Fantasy Flight Games do not permit proxy cards, so ask all your players to bring with them their Shifting Sands story cards - and if at least half the players do, then you'll have enough for everyone to use.