I was in the same situation 3 months ago. I spent 6 weeks looking at Cobras and couldn't find a decent one. Either the owners didn't take care of them or they wanted way more than they were worth. I ended up at a dealership looking at a 97 that ended up being damaged and when I went to leave a load of '00 GT's came in and bought mine that day. I only plan on doing basic bolt on's to get into the mid 13's nothing that will void my warrenty. I also drive 75 miles round trip to work every day.
If you can find a good shape Cobra for a reasonable price get it but if you can't the 99-00's are nice also. Regardless with which one you go with they handle and drive so much different than the 79-93's.
Just my .02
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