The reason all of the characters model parts are on top of each other (I'm guessing) is releated to me not using the animation info. I assume that they're using skinned and boned models so each model part's position is governed by the skeletal information. This info is probably in the MESHOPS or TRACKDEF sections somewhere (you can see these in SPK files), but I haven't been able to figure out what the data means.
The different parts of the models do have an xyz offset, I didn't miss it, it's just zero all the time for non-zone models. Even when the offset is applied to zone models it didn't turn out correctly. Zoneconverter manages to put the zone geometry in the right place, but reading through that code makes my head hurt
Regarding transparency and animated textures, I've not even looked at the MDF (Material defenition file) files, which is where that info would be kept. I discovered quite early on that the MDF filename was the almost same as the texturemap it contains (CUB0000_MDF uses CUB0000.bmp) so I cheated and assumed that
What I really should do is open up CUB0000_MDF and pull the material data from there. Texture transparency should be quite straight forward, I could probably put in a toggle for that so you could do it manually.
I found another reason for textures not displaying too, I can only pull textures out of the current S3D file that you're viewing. Some models, and I think all the zones do this, have their textures in another file. It had been puzzling me that some textures dissappeared when I switched over to using the S3D files rather than disk files, looks like that was why.
K.