if you get an auto tranny, definitely look at swapping to 4.10 gears, and probably a shift kit or a flash tuner to firm up the shifts. it will give you more perofrmance, plus add to the fun factor
an x pipe is known to be raspy. If you go w/an H pipe, you will get a different tone, but the mufflers are what gives you the sound. Just swap to an o/r h pipe and see if that sounds any better before throwing out extra $$ for a new 'cat back' system, too
an O/R H pipe will give you the sound you are looking for vs. what you heard/disliked about an X. Granted, it all comes down to personal choice, but most seem to lthink that OHVs and SOHCs sound best w/an H pipe, and the DOHCs sound best w/an X pipe. My choice would be the ProChamber
I don't know if you've considered this, or if it's an option for you, but the '03 and '04 Cobras come w/forged internals from the factory, plus they are easily upgraded to 500+ HP w/a few of the typical bolt ons.
traction will definitely be a concern. Are the 3.55s not enough. If you are looking for a little more punch, have you considered a pulley swapand a new tune to match?