Very interesting thread Skwasjer, this is just the info I needed at the moment as I've been experamenting with some skinning of my own. I had kinda figured out what you put in the first post over the course of a week or so!
Something that I find a bit of a shortcoming in the process that SH4 uses to skin the ship models is that the O01 files are pretty low res compared to the T01 files.
So if for example you wanted to place some writing on the side of a ship, it comes pretty fuzzy looking.
Is there a way around this?