The top mods on the to-do list on a budget in my opinion are:
1) CAI/tuner combo - will really wake the car up, get rid of throttle lag
2) Aftermarket muffler - get rid of that restrictive stock muffler
3) Gears/tlok - better acceleration while getting rid of the peg-leg and put power to both wheels.
Look at it this way: what will you be able to use and appreciate most, most often?
The tuner/tune will be pervasive every time you turn the key, and will transform the Mustang experience. A CAI is only worth it in High Performance situations, Wide Open Throttle or really fast driving. A K&N drop-in air filter is about $40.00, and although I'm not convinced it is an improvement over Original Equipment, it's cool to put that "Stop" sticker on there and watch the service writers' expressions.
So you've got the tuner/tune from B@MAchips or equivalent, about $410.00. The V6 muffler is notoriously restrictive; almost anything will be an inprovement, and duals, while very nice-looking and -sounding, add very little in the way of performance. GT take-off mufflers are inexpensive, the right-side one fits with no problem on your stock pipe, and if you get the set the left-side one will be good when you finally succumb to the drive for duals. $65.00.
Plus the $410.00 = $475 from your $1,000.00 = $525 to spend.
What else can you enjoy at all times? GT takeoff sway bars. Even if you're Pony-Packaged, the bars are thicker and make a lot of difference. $100 + $475.00 = $575.00, $425 to spend.
None of this stuff will work as good as it can unless you apply it to the ground: yup, Tires. Get something of the same diameter as the ones you have, but one or two sizes wider. Ideally, wider rims, too, but just the tires will be a fine complement to your other "mods".
That approach has resulted in a Very Nice Mustang at Relatively Low Expenditures. Works for me.