I got 3.73s in my coupe, and it was easy to use the SCT tuner to compensate, when running a tune. I wanted to be able to run the stock tune on the street, and compensate for the gear change as well. No dice at the dealer. They messed with their computer and my car for an hour, and decided they couldn't do it.
I changed the K&N CAI for a FRPP "Bullitt" item. The "stock" tune became the FRPP tune, and the FRPP "ProCal" tuner allows for gear changes and tire revs per mile compensation in the stock - and CARB-legal - tune. The SCT Bama tunes will go on over the top of the FRPP tune. All is well.
ADDED: 2014 GT 5.0A conv. black: electronics, comfort, security, CA plate (FLICK U); assembled 06-13-2014, delivered 09-25-2014; odometer today (03-21-2016) 4,321.5(--> DELETED --> 2013 5.06M coupe, black:: Odo LAST day (09-25-2014) 7,975) (--> DELETED --> 2008 GT/CS: Odo LAST day (10-22-2012): 9,719.3; #2075 of 2509 convertibles, #560 of 718 in Ebony. 2009 GT/CS: Odo last day (09-08-2012): 12,000.1; #34 of 1705 coupes, #3 of 377 in Performance White. <-- DELETED <--)