That's really not much money, but you can get a nice start to a solid engine combo with it. My personal choices if I had $1000 and a stock 'stang:
Free mods - remove air silencer, advance timing, some weight reduction
K&N filter and make a cold air intake
3:73 Gears + install = $300-400
Underdrive pulleys = $100 max
Mass air meter = $200 approx
Throttle body = $180 approx
Those will add some speed to the 'stang. And when you do upgrade intake/heads/cam, you won't have to worry about restrictive MAF or TB
But those are just my personal preferences. You could also look at lowering ur car, or new wheels/tires, new hood, etc. Also, tmoss ported lower intake is pretty cheap, so are thumper heads, and you'd get a nice power increase with those.