I've found out the creators used silo3d for the cage meshes, then 3ds max and zbrush combined to 'sculpt' the models, and exported from max in a custom / propriety format where they wrote a plugin but I'm new to this and you guys are awesome lol
ign dev blog page: http://blogs.ign.com/Ubi_Naruto/2007/10/12/68798/
silo3d forums: http://www.silo3d.com/forum/showthread.php?t=12815
modeller's gallery: http://www.khalys.net/BOOK_2007/Naruto.htm
You can kind of guess the poly count if you look at that guy's other works on the same site
So I got 3 shape files and I can see there is a good few lines the same on all the files (not sure how long exactly) and definitely lots of bone / joint names in there, and animations right from after the header (raged, neutral, hurt)...it's really confusing as they're different
also there might be some kind of texture name further down but I'm not bothered about textures 
http://files-upload.com/files/684448/gaara_shape.txt
http://files-upload.com/files/684453/haku_shape.txt
http://files-upload.com/files/684467/kiba_shape.txt
http://beta.freedrive.com/member/viewfolder/30808
hope this information helps, i just want to be able to import into any modeller to take a look =)
there's bone / joint names going down to offset ~9300 / ~2454 hex
(Head, Crotch, Forearm, Finger, Armpit, Cloth ?, Ruban?...)
and 2/3 of the way down the file you got animation names (maybe?), ~270000
(Energy, Rage, Shield, ChakraControl, Haku's mask 'prop')
so they are actions / attacks I think.
I have no idea about offsets in the headers I can't seem to understand it yet, but it doesn't look too hard to figure out for people who know what's what, any help is appreciated and thanks for reading.