I went from a bolt-on modded, geared 14.1 sec. 2V '98 to a bone stock '98 Cobra...what an amazing difference!
High 13s to low 14s stock, mid 13s with tires, gears and/or bolt-ons. This engine really likes a centrifigal blower and responds well. Mid to high 12s w/ proper setup and driver with just a street blower and necessary traction mods.
I plan on supercharging and opening the exhaust up some and not messing with anything else not related to putting the power to the ground.
These engines love to revv, it's cool taking it to it's 7000rpm fuel cut. You won't have the same low end torque, but feeling the power push you further into the seat as the RPM climb higher, to 7k is a really cool feeling. When I first got my Cobra, I was shifting at 6400rpm unconsciously b/c that's what I was used to. It's really cool to stretch the Cobras legs and feel the power.
I have 4.10's in mine and they are a very streetable gear. If you are going to do a lot of bolt ons, I'd say 4.10's would be good. 4.30's would be streetable too, but more track oriented.
You don't need to build the rear. The stock rearend is very strong from the factory.
As far as exhaust, X-pipes are going to give superior peak power over H-pipes. If you want a cheap aluminized pipe thats built well and fits really well, get a upr x-pipe for $140. www.uprproducts.com It's basically just the two pipes merging together in the form of an x, I don't know how efficient it is compared to other "chambered" X's like bassani's, but supposedly it's good. As far as a catback goes, Bassani/Borla/Magnaflow will flow the best, but are stainless steel and cost out the @ss. I believe they offer some aluminized catbacks though, but they are still pricey. You can get a Flowmaster American Thunder catback for hundreds less, for almost half the price, and still get similer performance gains, albeit not quite as good. The sound is awesome though, although I heard a Bassani today on an 03 and it sounded sweet too. Can't really get a bad sound with the stang.
I would look into a Steeda Timing adjuster as well. A friend of mine saw his buddy pick up 6rwhp/9rwtq by advancing the timing 3 degrees. (conservative). I was THIS CLOSE to picking up a used t/a for $60. If you can find a good deal, IMO it's definately a good buy, considering you run 93 octane religiously.
Good luck and keep your questions coming. I will try to help out with the limited knowledge I have.