Sam-
Get a 99+ Cobra WITHOUT the spoiler. Those are so wicked looking without the wing. I've never liked the spoilers on the Stangs (way to tacked on looking). Get a nice 1.5" drop and the car would be perfect. If you are more interested in the 1/4 mile, forget the 99+ Cobra. The independant rear end is crappy for the track. The live axle in the 98 and below is far better. Rememeber that those 99+ Cobra half shafts are supper weak. Gear changes in the 98 and below Cobras are FAR easier and cheaper too. No less than a 4.10 gear. Anything less and you're wasting your money.
BTW, keep in mind that anytime you modifiy your car, you're asking for problems. If you really want true daily driver, stick to the simple and effective bolt-ons. Steer clear of nitrous, forced induction, heads, etc. 12s is plenty quick for a street car and 12s are easily attainable in any 99+ Mustang with a few well selected bolt-ons.
Dave