I had a look at the "modelmine" file, I just noticed only now.
The file is nicely structured a header and relative offsets to subsections, and each subsection has a similar header. The only exception seems to be the (probable) model data starting at 9800, this may be hardcoded in the game code. Same for 14800 which is a header containig pointers to the other subsections until the end of the file.
Section 00009800 ~ 00014800:
the first $20 bytes are a header. The first value may be the number of sections, the others are relative the offsets (relative to the beginning of current section, that is). Some of the sections are similarly split in subsections. I have no clue what they may be
Section 14800 - end of file:
header as above; the "unknown" sections between weapon textures are certainly weapon models.
for example, the first is at 15dc8. From there:
0-7 unknown
8-11 offset to vertices section
12-15 probably offset to unknown section (at 15df0)
this seems to be made of groups of 4 bytes. I nocited some textures have weid coloring,
maybe models are textured AND color shaded. They could be RGB values. (but the 4th byte?)
16-19 probably offset to unknown section (at 15ddc)
The vertices section is a Cyber said above: groups of 4 2-bytes values, the last is 00 00. Vagrant Story is like this both for characters and weapons, but your model data here seems different.
Note how the first value also is often 00 00 or little more, that's because of the flatness of weapon models. However the last value sometimes is 01 00 or 02 00