I am in your same situation right now....looking for a Cobra around those years.
Your right, the 03-04's are pretty expensive. The cheapest I have found them for is $15000. But they are supercharged and also take premium fuel thats why I am not getting one. You probably know that. A stock one will run 0-60 in 4.5 seconds and 1/4 mile at 12.9(or close to that).
No cobra's made in 02. (unless you find a cobra R, which are very rare and super expensive)
The 01's are very fast. They run a 0-60 in 4.8 seconds and 1/4 mile in low to mid 13's. But still they are quite expensive. I doubt you will find one for a whole lot less than the 03-04, unless its been beat.
In 2000 only cobra R's were made. Good luck finding one of those. They are very rare.
In 1999 they made the new body style of cobra. Ford said it had 320 horse power(just like the 01 has). But turns out it was the same speed as the 94-98 cobras, or some people say its less powerful than the 94-98. But if you find one that was recalled then it should be up to par with the 01. But I am guessing most of them are not.
The 96-98 are fast. Just a little faster than a 99-04 GT. They run a 0-60 in 5.4 seconds, and a 13.9 second 1/4 mile. You can easily mod them to be faster. With 3.73 or 4.10 gears, head swaps, CAI, and modified exhaust you can get them down to probably close to a 5 second 0-60 depending on what you do. Throw a supercharger/or turbo (like the 03-04's had) and you'll probably be running pretty close to them. But you'll have to do the premium fuel thing.
Good luck finding your cobra
I think I might be settling down with a 96 as soon as I sell my 98 GT.