Nice, sounds like a interesting project, How are you planning to put the files back into the game or is this also a secret part of your project ?
well the folders for FF9 are (this info was taken from Zerox)
0 - Status/Menu/Battle/... -Text and random stuff.
1 - Misc Images (Logos, Fonts, World 'mini' Map images, etc).
2 - Dialog Text
3 - Map models (Mini-zidane, airships, save point moogle, tent...) and, IIRC, the map texture.
4 - Field models
5 - Monster Data (Part I, stats, names, etc).
6 - Location Data (Dungeon, Cities, etc).
7 - Monster Data (Part II, 3d models)
8 - Weapon Data (including models)
9 - Samplebanks and Sequencer Data (ie music).
10 - party members Data (including models)
11 - Sound effects
12 - World Map Data.
13 - Special effects (magic, summons...)
So the folder you are after is folder 4, hope this helps, also if you want to view the backgrounds i know there is a tool for doing so, when i get back later i will dig it out for you if you want (i am about to go out right now), or you could try searching this forum since i did get it from here (i can't remember who made it though, possibly zidane_2)