ASSUMING nothing has been modified cosmetically...
1999 can always be identified by the 35th anniversary emblem. 1999 Cobras had MUSTANG debossed in rear bumper, SVT COBRA badge on left side of trunk. The 99 35th anniversay edition had a hood scoop and side skirts that would show up on all GT's in 2001. They also had the center portion of the hood blacked out and a blacked out trunk panel
2000's got the running pony (V6) or GT fender emblem, GT also has GT emblem on trunk
All 99/2000 have the wrap around spoiler, chrome housing headlamps and no raised hood scoop. The side scoops are open "C" scoops. They also have single DIN radios and a cup holder "insert" where the ash tray was on 94-98. The rear defrost switch is located under the headlamp switch.
2001 was a transitional year. Early build 01's were just like the 2000 but there were very few produced. The Bullitt model introduced the raised hood scoop, "enclosed" side scoops, smoke housing headlamps and the infamous Bullitt wheels. All of these found their way onto GT's and Pony Package V6's. On the inside Premium GT's got taller, adjustable headrests and double-DIN radios. The cupholder now looked like it belonged as part of the console. Other minor switchgear changes included the fog lamp switch relocated into the shifter bucket next to the traction control off switch and rear defrost switch.
The Bullitt looked like a GT without a rear spoiler. They also had rolled exhaust tips and unique, retro gauges and seats like the 01 Cobra except for a comfort-weave style pattern. The side scoops were also the open style like 99-2000.
The 2001 styling carried through 2004, with the 04's getting the 40th anniversary fender emblem.
The 2001 Cobra has seats with thicker bolsters, chrome wheels and the word COBRA debossed into the bumper with just a small SVT badge on the left side of the trunk.
The 2003/2004 Mach 1 had the shaker hood scoop, chin spoiler, mesh-grille delete, appropriate striping, rolled exhaust tips, unique wheels and an interior very similar to the 01 bullitt with the retro touches.
The 2003/2004 Cobra has unique front and rear bumper covers, side skirts, hood, color-keyed mirrors, seats, spoiler and wheels. If you can't spot an 03/04 Cobra as different than any other new edge Mustang, you probably need to turn in your keys as a late model Mustang owner.
I think that covers everything that is important. I can't believe I just did that off the top of my head, haha.
AND, for the record, NO Cobra came from the factory from 1994-2004 with a Cobra grille emblem. It is just a popular change, like I did with my 97.