I've been meaning to update this thread, but at least I can share a little of my progress.
I've managed to match the majority of functions from the game.MAP symbol map from the EUR version to the layout of the US .dol file. There is also a game.MAP file on the US version, but this is for a debug build, so it wasn't very useful. For some reason, the EUR symbol map matches the US version better than the EU version, so my guess is that the symbol map is from an early compile of the US version, before they started work on localizing it.
The symbol map matching was done using some clever heuristics, so there are 10~15 functions I couldn't match, but otherwise, it is really impressive IMHO. Resulting map for US version is here, which can be loaded into Dolphin: https://bpaste.net/raw/dc90c3bd12d9.
I'm almost done reverse-engineering the animation file format, just some edgecases to figure out. I've also started exporting to .dae, so now the results can be viewed in Blender:

I've also done some work on visualizing maps, including a very early prototype map...
Hope I'll have time to revisit that soon!
EDIT: Also very cool work Rinji! How did you manage to get eye UVs working, by the way? Haven't looked at that yet :o
EDIT2: I guess I'm going to make this my dumping ground for discoveries I haven't cleaned up yet.
f008.chm prototype

Prototype texture:

f060.chm prototype map

Video: https://gfycat.com/FlickeringDecimalAmbushbug
m000_root.chm debug map

Video: https://gfycat.com/SolidFormalAstarte
m077 early c700 character

(final left, early right)
m078 early c800 character

(final right, early left) |