I'd get a throttle body along with a intake manifold/plenum. Boss 302 is a good pick, but if you have the money and want the extra power get the ford racing, along with the recommended TB. Not much you can do to the 2011-2014 mustangs, to keep it naturally aspirated, only thing you can really get other is some headers, and a mid-pipe along with some high flow cats. Oh and you can grab yourself some underdrive pullies, also i'd grab these injector is you plan on getting a new intake manifold
Ford Racing Mustang EV6 High Flow Injectors - 24 lb M-9593-LU24A (87-14 All) - Free Shipping (Guessing you like AM) . Now drivetrain wise, grab yourself a new one piece driveshaft; they are more on the expensive side but are way better. Last thing, bama tunes aren't the best.... I'd take your car to a performance shop and have it dynoed and tuned.