With the gears you do not have to replace the entire rear axle its just the gears. As for which ratio you want either 3.31 or 3.73 it depends on what you want from them. A higher ratio will give you much improved acceleration with 3.31s being faster than 2.73s and 3.73s are faster than the 3.31s. The 3.73s are really popular and will make your mustang feel completely different since higher gears put the rpms closer to these v6s power bands thus quicker acceleration. However, higher gears come at the cost of your mpg. You wont notice a huge change around town but you will definitely notice a difference on the highway. New gears also need a tune to recalibrate your speedometer. In short 2.73 = high mpg all around,slowest acceleration. 3.31 = decent mpg all around, and better acceleration. 3.73 = worse mpg (mid 20's i think), but awesome acceleration.
With the headers if assuming you are talking about long tubes and if thats the case you will also want to add a shorty mid pipe so that everything hooks up. Also depending on your emissions laws you will want either high flow catalytic converters or an off-road mid pipe which deletes the cats, mid pipes come in either an X or and H. A warning tho combining long-tubes with an off-road mid pipe and the borla ataks they will be insanely loud, the s type might be a better alternative but of course its all personal preference. Long tubes also need a tune to get the full benefit of them and to get rid of the error code do to the moved o2 sensors i believe.
As for suggestions, I would do a CAI, a catback exhaust of your choice, and a good tune either bama, mpt, or lund. If you're feeling ambitious you could even throw in 3.73 gears and then see where you stand to do the long tubes afterwards but thats just me. That combination off mods would be pretty awesome. Sent from AutoGuide.com Free App
2011 Race Red GT/CS: current
MGW race spec shifter, Borla ATAK axle backs w/ resonator deletes, Boss Intake Manifold w/ Steeda CAI, stainless power longtube headers, driveshaft shop carbon fiber drive shaft, ACT twin disc clutch.
2014 Race Red V6: sold
Airaid Cold Air Intake, pype bomb axle backs, bama 91p tune, ford racing 3.73 gears, Barton short throw shifter, Mac ceramic shorty headers.