1.) Rear End Gears:
No Less than 4.10's almost every person who buys 3.73's regretts it and 3.90's is a split crowd if you drive on the highway over 75 MPH alot, most stock Mustangs come with 3.27 gears and 5th gear is rendered useless for most driving. The best fitting durable brand for Mustang rears has to be the Ford Racing set.
2.) Exhaust:
Some Mustangs come with a total of 6 in pipe units (cats and/or resonators) this is a very restrictive mid pipe from the factory, I think the mid pipe is more restrictive than the cat back but you should do both at the same time. Some brands to try to stay away from are BBK's X pipe and if you hate rust stay away from flowmaster and Mac
Headers: On the modular engines, the stock manifolds flow pretty well so unless you are going to do some major modifications (ie cams, heads) don't bother, if you must get headers go with long tubes
3.) Shifter
Mustang shifters are so sloppy it's ridiculous, that is the second modification I did on my Mustang and it made the world of difference, MGW is my favorite shifter and have the firmest centering springs on the market, also it has the shortest throw. Pro 5.0 is a close second
4.) Intake:
Remove the Air Silencer in attached to the air box and put a drop in high flow filter, Intakes are not worth the money for the gains they give, the gains are comparable to the drop in filter and removed silencer. If you must get and intake Demolet makes a very good one
5.) Throttle Body/Plenum:
These will give you decent gains but it is up to you if you want to spend the large amount of money for them. Best combo on the market is the Accufab TB/Plenum but all others are ok...ie BBK, C&L
6.) Under Drive Pullies:
Not worth the money but if you are scraping for all the ponies you can get they are worth a little under 10 RWHP. Stay away from sets with piggy back crank pullys (BBK). The best set on the market is by March
7.) For the track mods:
Drag Radials....BFG KDWs are good but the choice is yours
Remove your spare tire and jack with any other excess weight
If you want you can remove your passenger side headlight for better air induction