the '01 resolved performance issues with the '99 (hence no '00, other than the 'R') (see
Lack of Power in the 1999 SVT Cobra for example). '01 also has 'cobra' on the rear bumper, and the rear spoiler changed. not sure about interior changes, that may have been when the two tone seats were added.
i've had mine for four years, no problems (25k miles now, daily driver). you'll want to upgrade the catback for sound and performance, many owners add CAI and gears (4.10). lowering springs are a nice touch, too, I don't understand the height of the stock car. i have eibach prokit, which are still an inch too high in the rear with stock profile tires.
If you have the money the terminators ('03/'04) are a nice upgrade, I still think about it, (and still don't have the money.)