Unless something is worn or broken - keep the car stock if you plan on auto-x (maybe just new shocks/struts). A stock Mustang/pre-'03 Cobra's class is F-Stock.
Some sticky rubber like the Kumho Victoracers are a great mod, beginner or not.
Keep your car stock. I say this b/c no matter what you do to your car, if you have no experience - you will get romped on no matter how much hp or $$$ you invest. I've been there as well as every other auto-x guy/gal.
Keeping the car stock will teach you the shortcommings of your 'Stang. As you get more seat time, you'll become a better driver. After a while you'll out drive your car and you will modify your car to accomidate taking turns quicker. (or in my case you start breaking stuff which is a sign that you are getting quicker and you need to fix it so you might as well put on the good stuff!)
This is where you can start changing things. But keep in mind, the SCCA has some pretty strange rules. Get a '04 rulebook and read about car classes.
And if you are bent on getting springs - I recommend H&R Race Springs, MM c/c plates and either Bilstein or Koni shocks. Do not do one without the others. Welcome to E Street Prepared!