The IRS was weaker on the 99 Cobra, it has a 28 spline, the 01 has a 31 spline.
The "fix" on the 99 should have been done, you can call a Ford lot with the vin # and they can tell you if it's had the "fix" or not. If not, they should still do it for you, but make sure they will.
Some 99's...