Can some one help explain the differences between 1999, 2000 and 2004.

What year is the 40th anniversary edition... is it 2004 or 2005.

 

99 has 35th anniversary edition V6 package includes a GT look alike package that gives it the exterior appearance of one (don't know about fog lights).
2000 is identical just no 35th package available.
2001 has minor interior changes. The most significant is the center console is revised to make the drink holders more useful. minor change in harmonic balancer for V6
2002 I believe goes through a tranny change in the autos and manuals too (?) regardless of engine
2003 smoked headlights and a new wing spoiler. V6 mustangs have the option of the GT hood scoop on them now as well. Overal front and rear bumpers on both cars are slightly smoother in appearance.
2004 Bullit rims available for GT, V6 gets a revised hood with no scoop at all, late 04 gets 3.9L motor, GT retains same hood it always has no real changes I'm aware of.

I might be a little off on the what specific year the changes were introduced but those are the main (major/minor) changes

I don't know much about the Cobra changes other than 2003/2004 came with S/C and was a full second quicker 0-60mph and 1/4 mile pass than the previous model year it was built.

40 anniversary is 04.

 

Overall the above is correct, but with the following changes:

2001 GTs got larger hood scoop, 2001-1/2 GT gets Tremec 3650 tranny, rear spoiler/wing change, Bullit rims available on GT Premium.
2002 -- Smoked Headlights, Running Horse on fender instead of "GT" badge.

2004 - 40th anniversary. Special Edition with badging, Dark Red metallic paint/gold striping, "arizona" gold Bullitt rims.

Go to The Mustang Source for full details of model year differences.

 

In 1999 the standard GT rim was 16" also the 17" were optional.

In 2003-2004 the GT had polished 5-spke wheels as an option, they were just like the 99 Cobra's but with pony center caps.

The pony emblems on the GT fenders were gone after 1999 and returned 2004 with the 40th logo.

One really minor change that no one can really notice is that 1999 and some 2000 have a black filler panel between the rear bumper and the impact foam, after 2000 the foam is visible but painted black. Look in the slots between the exhaust tips in the middle of the bumper.

The honeycomb in the hood scoop and side scoops also changed size when the larger scoops were added.