$1000 Budget?
4.10 gears <$200
Install <$200
Short Shifter <$200
Take the rest and spend it on Test and Tune nights at the track. I got started into Mustangs in my teenage years and thanks to being broke and some good advice from people like the guys on this forum, I started racing it before I started modding it.
You could throw $200 bucks at the car here and there, with weak little mods like UDPs, a Plenum, TB, CAI, etc. In the end, the gains they provide are nomimal, with little to no seat of the pants feel. You could drop $1000 on one big mod, but chances are you'll be missing out on the proper peripheral mods that compliment it. (ie cams, but no tune, free-er flowing exhaust, etc.)
In the end, you want to be able to understand how quick the car is as it stands. How it responds to the weather, or to little things like sneezing between the 2-3 shift. Without timeslips, how "fast" or "quick" a car is a "science" practiced only by benchracers and forum-addicts. "I think I edged out that LT1 Camaro because of my timing adjuster" is not the same thing as "this mod gave me a 1 tenth of second gain and half a mph compared to the last time I ran it under similar conditions."
After you've baselined the car, if you want to throw little mods on the car, feel free. At least you'll be able to realistically determine what gains, if any, were provided by each mod.
I suggested gears because they're your best bang for the buck from a $$$ standpoint and from the seat of the pants. The car will really wake up and be alot of fun to drive. The short shifter also inspires alot of confidence, and quick shifts make a difference at the track.
Keep in mind this is just one guy's opinion. I just loved knowing that I had squeezed every last tenth of the car before I threw some dough at it. Also, you'd be amazed how a few trips to the track make you a fairly proficient test and tuner. There is nothing better than whooping up on a bolt-on'd and drag radialed GT with your stock GT at the track, simply because that guy hits the track once a year, and you're there twice a month.
Good luck.