I resisted long enough time for my $.02. I agree that the 93 Cobra is special and I sure wish I had one at 16 but we aren't all that lucky. I'm 23 and got my first mustang a 67 coupe with a 289 when I was 17 and I traded it in for my current 91 which was bone stock when I got it. I learned alot constantly fixing the 67 and it carried over to the 91. I can do almost everything I need to and it is very gratifing when your at the track blowing the doors off cars that have more motor work and have been done by professional shops, I have a friend that had his car dropped of stock 14.9's and picked up running 12.0's, anybody with a little money can do that.
As for keeping the Cobra stock, here is the approach my dad took with his 93 Cobra. He wanted a stealthy car so he extrude honed the intakes, port/polished the stock heads and added a cam, Pro-M mass air meter, and a Speedbrain computer, it looks stock but runs a lot better. 12.70's @ 107 stock suspension on 9.5" ET STREETS. I say choose your modifications wisely but don't be afraid of it, if you have questions ask, no question is stupid if it helps you out
Good Luck and happy wrenching
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My Ride Check Out My Site 91GT, Holley SysteMAX II Kit-Heads 2.02" x 1.60",Full MAC exhaust 1-5/8" Long tubes, 2-1/2" O.R H-Pipe, 2 1/2" cat back, 12" K&N Filter, RNH PERFORMANCE Ram Air, Ron Davis Radiator, Full Suspension,3:73's, Welds, Best on new motor-12.60 @ 108, no traction 1.98