I spent sometime over the summer trying to crack the format as well. Here's what I found hope it helps.
If you load cheat engine's memory viewer and view the games memory at address 0x20801000 the entire bin file of whatever character you're playing should be loaded into memory there and you can make live edits.
I did most of my research on the file EREKIDAT.bin in the PLAYER.afs archive. So the follow info comes from his bin file. Maybe some of it will be applicable to the stage files.
The bin file separates the model into segments for each body part. Each segment has its own set verts, uv, and triangle indices. However the indices of model are the same for all segments. So indices 1 and 2 refer to the same vertices for all model segments. I do not know if all vertices are the same for all segments.
Also there's two models, maybe three models per character. One for character, one for outline, and another for the shadow.
The indicies are packed right next to uv coords the format is as follows
[size in bytes,purpose]
before the indicator there is 2 bytes that determine how many groups there are. It also used to determine the facing direction of triangles
[2 bytes, IUV Group count]
[2,quad or tri indicator] if tri the next part has 3 groups if quad it has 4
Index UV Group
[2,vertex index][2,UV Cooardinate X][2,UV Cooardinate Y]
Here's an image to illustrate it
all of these offsets map 1:1 at 0x20801000 in game
pink is a ARGB color overlay
brown is a different type of indicator. I think it determines whether or not to render the tris or to use them as uvs of some sort.
purple is the tri/quad indicator
green is IUV Group
orange is the number of tris/quads to render this one is funny it does not always add up to this number
yellow is like purple but its negative and the sign value determines whether or not the tris are front or back facing.
Vertex and Normal are right next to each other as well
[3 floats,XYZ position][3 floats,XYZ Normal]