I unpacked and repacked using GARbro at your link.
Start up tool and Extract 3d.npk (check Extract images)
It is assumed that various files are extracted under the media folder
Modify the model or textures as necessary.
Back to GARbro,select media folder,select create archive (choose Archive format NPK Archive options Sonicomi)
So created 3d.npk I have no problems running the game
Although it is good to be of some help