So here are my findings that could be useful to anyone who wants to improve the current Noesis script. It's not 100% accurate, but it's a good majority of what's documented. The VUG files first starts out with the header and total file size, then the number of VU1 or VU0 models that are inside, and then the index of offsets where the said files are located. The header of the VU1 and VU0 files are mostly the same with the first 4 bytes and then the file size of it.
And then you have the file headers inside the VU1 files. The file header is always "04 04 00 01". After that comes 4 bytes which are the version of VU1, either "00 80 02 6C" (52 bytes) or "00 80 01 6C" (36 bytes) and they both behave differently from each other. There are some versions where the bytes are "## 00 04 6C" or "##" 00 01 6C", but I don't know what they're for. (Maybe bones? Who knows.) After those 4 bytes comes an early vertex/uvs/normal count for the mesh that it searches for. And after that there's the file ID in bytes "00 40 2E 30" for the regular meshes that the current script can grab, or "00 C0 2D 30" for the rest of the geometry that the script misses (The holes!). After that comes 4 bytes of "12 04 00 00" which is mostly consistent, and then there's 4 bytes after that are different from the two versions. "00 00 00 00" for the "02 6C" files, and "0C 00 00 00" for the "01 6C" files. If the ID is "00 C0 2D 30" then it's a "0B" instead. After that there's one more set of 4 bytes that are different from the versions too, "05 01 00 01" and "04 01 00 01". And then comes the actual mesh data. Listed in the picture down below is a comparison between the two versions of how the vertices, uvs, normals and faces are handled as they have one slight byte difference. VU0 models have still yet to be documented as there are some VU0 models inside some of the VUGs that are of a character's face, miscellaneous objects, etc, and are handled completely different compared to the VU1 models.
But anyhow, I hope this helps out a bit for improving the mesh script. Best regards!