Best of luck with your status matching efforts. I have a feeling that Southwest will bend the elite qualification rules to keep as many AirTran customers as possible.
And likely vice-versa. Southwest status unlike Airtran is calendar year. Airtran was a rolling period. So the Dec 31 end date was set by their system unless you happened to requalify for 2013 by flying a bunch on Southwest. The two systems are not yet connected for status on both without manual re-entry.