@Ghanmi: Learn to use Crystal Tile 2. As you see above in my last post (glove), CT2 is capable to edit the 3d textures very well.
You maybe have to get familiar with some formats, compressions and maybe just paste a file in hex mode inside a NSBDM.
CT2 is capable to edit the NCGR/NSCR (NCLR is the palette and nor the tile nor the map)
Your problem will probably be that many images use NCER and not NSCR so you will probably not get very far.
By the way, I wonder what make you think you will be successfully translate Death Note or Ninokuni if you don't even get a table done. Don't you think you should maybe start with something much smaller and maybe in english??
Just to prove something: http://gbatemp.net/threads/ninokuni-shikkoku-no-madoushi-translation-project.310214/
, you really think you are the first one that attempt to translate Ninokuni??
Oh, I just remembered that most graphics in Ninokuni are compressed in a non standard way so you have the same problem as you other project. When the time will be right, the right persons will come together and translate even Ninokuni.
By the way, the same apply to the Death Note games: http://gbatemp.net/threads/death-note-games-translation-project-need-help.259246/
Sorry to be harsh but romhacking / games translation is not the same as translate a TXT file.
@Nix_Aether: Console tool is a good tool but doesn't yet support editing so it's probably not good for your needs.
Lowlines is working on a new version of CT but he doesn't say when it will be ready.