Rev, when the original set of 1999 DOHC Cobra's were released, they were advertised as 320hp. In reality, they were making about 300. The problem was a last minute intake manifold change that proved to be mismatched. The problem was corrected with a "fix" and many of the DOHC Cobra's were putting out closer to 340hp at the crank after that.
Ford killed the Cobra under the guise of making sure everything was correct partially through the production year, if I remember correctly. There was no 2000 Cobra, just the overpriced Cobra R.
In 2001 they released the standard limited edition Cobra that was making more than the advertised 320hp, again about 340hp like the good "fixed" 1999 Cobra's.
Ford again killed the Cobra for the 2002 model year, citing they wanted to make sure the rollout of the 2003 Cobra was a success.

So there was no Cobra in 2000 or 2002. All Cobra's after 1998 came with the IRS. 2001 had beefed up half shafts I believe. Obviously the 2003 does as well.