It depends how much money you want to spend. You can spend a little money and get more clarity and a little more bass. The stock speakers in the shaker 500 are crap, especially the subs in the doors. Replacing those alone will give you more bass but you will want to get an amp to power them all.
There are a few options for the 5x7's in the doors as well. I have the infinity's (They are in my sig) they need to be powered by an amp, but they are much louder and clearer then the stock. There are other brands that arent so harsh on the tweeters though. You definitely will need to upgrade them or you wont hear anything over the bass.
As far as the subs in the trunk, you can rip the box they have in there out and get a custom box made. Most audio shops sell mustang boxes. (Get a ported one if you want people to hear it outside the car) Get Dual 12" subs. I would go with Kicker if you want more low end bass for rap, and if you like tighter bass for like rock, I would get MTX. Match up the subs you buy with an equally powerful amp. Probably will need one with at least 750 RMS. Kicker has really good amps, which are way under-rated and seem to last forever. Make sure to get a D-Class amp for the subwoofers though, because they have a higher efficency then Class A and B and wont punish your altenator as much. And depending on how many watts you need to push, you should get a capacitor and a deep cycle battery like the optima yellow tops so your lights wont dim at night and your car wont lose power.
Also, dynomatting the trunk will add about 3dB to the bass alone without even changing out anything.
Dont let the car audio guys fool you with numbers though. A 150 Watt subwoofer can create alot of bass. To double the power you feel from 150 Watts, you have to multiple the watts x10. So you would need a 1500 Watt sub to just double the power you feel from that little sub. Or you can get 2 subs
(Its Ohms Law). So, IMHO just start big, because you will want more if you dont.
REALLY Good Sound System for my Mustang? 
