Is your 99 GT a regular 35th anniversary or a special edition anniversary?
The regular 35th's just had the 35th emblems on the fenders, that's it.
The specials had the 01-04 GT sidescoops, black honeycomb panel on the decklid (which you have), two tone black/white leather seats with white stitched ponies, and the smaller hood scoop (which you have). They also had the "starfish" 5 spoke wheels with black inserts.
The 99 special anniversaries stock hood was the smaller hood scoop on the base forward facing hood.
The 01-04 GT's had the same base forward facing hood with the larger hood scoop on it (like the one I have).
My guess would be that you have the stock hood on your car right now.
Here's a link to some info about the 35th's...your car is fairly rare...only 1299 made in black.
Timeline: 1999 Mustang - The Mustang Source