The very first thing I would explore is to see if a Manny/ Bay type trade, using Josh Beckett is at all possible. Beckett is under contract for a few years, so maybe with a few mid level prospects, they can pull in a end-of-contract guy like Hamels or Greinke with a three team trade. Then, try to see if Ellsbury can land the team an ace. If not, get some elite pitching prospects or a #3 type pitcher to replace Beckett's spot, and sell sell sell.
Beckett/Ortiz have been absolute malcontents this year. Sell high. Shop Ellsbury for elite pitching talent, and see what turns up-- if nothing, it may make sense to wait till the offseason.
Besides those, they need to hold onto their core, and trade the excess baggage. Guys like Ross/Sweeney/Shoppach/Salty/Albers who have high value for desperate teams but aren't necessarily going to be allstar caliber players and/or see their contracts end soon. I'd be very much in favor of selling high on Saltalamacchia.
You could potentially trade all the guys above and leave yourself with a top 5 farm system, and the following core pieces in 2013, and a ton of money to spare:
Kalish
Pedroia
Agon
Middlebrooks
Lavarnway
Aviles
Crawford
Nava
Lester
Buchholz
Doubront
Bailey
Aceves
Bard
Melancon
Miller