start with door speakers see if thats good enough, there so cheap online it doesnt make sense not to swap them out ($50/pair for Polks).
Then if you want more loud or cleaner, your going to need a line out converter like the Audio Control unit which will allow you to tack on aftermarket amps and subs.
My whole system ended up costing me less than $500 and sounds unreal with the Shaker 500.
This is a potential option too. I didn't think the above would sound that great since i have doubts about the stock head unit frequency response range and signal to noise ratio but this guy says it sounds good. Might be worth a try and, like he said, not too much of a dollar investment...probably didn't take more than a day to install as well.
2012 Mustang GT Premium Kona Blue W/ 401A Trim
Electronics PKG, RR Sensing/Security PKG, HIDs PKG, Comfort PKG, Brembo Brake PKG, Glass Roof, Rear Camera