The first thing i would do (even with the flowmasters) is buy an x- pipe without cats(150-200) bucks on ebay. Get the mil eliminators(60 bucks) and this will keep yoour check engine light from coming on and it is the biggest single cheap upgrade you can do plus the sound is ten times better.
I would then buy an intake i like my k&N fpik kit (165 on ebay if you notice all prices will be for ebay) and it will further add to the sound. Dont think you will gain 10 hp from an intake and 23 from a xpipe and 10 from a muffler. Actual amounts are much smaller but you can feel them. then i would weld in subframe connectors (35 bucks) this will keep you from bending frame on down the road plus will save your ass if you play the smak a tree game. Nobody has won this game but i hear it is a hoot.
then you need a stall and a nos kit. the order you do it in is what ever the hell order you can find a deal. weld on those subframes cheap and you can feel em. Once you do all this lower your car and add nice shocks and struts consider your car a stage 1 upgrade.
When you want to hear about stage two (what i am doing to mine) just put up a post or holler young padewan there are lots who will help.

***look up notch 91*** his shop is called genium and about the only place that knows how to do the work properly and wont fuck you in the ass

buy a mustang mag before you start buying parts and make sure they are an easy install
long tube headers not a fucking easy install

gears help too but wait a while on em and i love my 390's