Tom's points sound right to my ear. They have a very good shortstop playing second and a starting 2d baseman as a utility guy. Seems like you need to unpack that value in a trade for what you need, which is another starting pitcher.
Really think this almost cries out for Espinosa and Morse to TB for Shields (add Mattheus too). Yes, Hak Ju Lee is their top position prospect, but worse comes to worst, you shift Zobrist to the OF in 2014 and go with Lee and Espinosa. Meanwhile, in 2013 you plug two positions for half the cost of Pena and Scott in 2012, and you simply start one of Archer, Niemann, Davis, or any of the other starters in waiting.
As for the ALR stuff, this really screams out for a 2 year plus a team option that flips to a player option based on games played or (if it can be done) some sort of repetition of last year's level of play. Something like it becomes a player option if in either year he repeats as a silver slugger, or more directly, hits 55 HR over he length of the contract and maintains an average over .275.