I personally feel that building a solid foundation is always a pretty good way to start, although I'm guilty of not really following that. Anyway, this is a great post to give you some ideas of bang for the buck mods: http://forums.stangnet.com/showpost.php?p=6144037&postcount=3
After you've covered the basics there, see what kind of money you have left over for performance. Adding an intake, or doing a MAF conversion isn't a bad idea if you have future mods planned, too.
That budget depends on if you are doing the work, or not.
Gears, 3.73's (that's gonna cost you minimum $500 with labor (you should not do these yourself)
Subframes, another non DIY project (unless you are a good welder, but this is not the project to test your welding skills), probably $250-$300 installed.
Underdrive pullies, $65
K&N panel filter $25
Full exhaust.
Equal length headers, 2.5 offroad X pipe, 2.5 Catback.
Don't buy cheap crap, or you'll be on here complaining about getting exactly what you paid for.
I'd rather buy used bassani or magnaflow stuff, than NIB parts from other companies.
That should come close to using up the entire 2 grand, depending on how you shop.
If you have any left over money, get the eibach pro lowering springs.
So i agree with most of the list that list GT1995 linked us to, except the electric fan, i think it's a waste of time, money, and adds unecessary headaches with no performance benefit. It does nothing, literally.