Scaling, rotating, moving should work fine. Ill get back to you on exactly what to do. Making a script the auto scales and moves probably wouldn't be the best idea. The clothing will be different shapes and sizes so you will have no guarantee whether it would put it in the right place. Manually doing it would be better. I also don't have JD or a lot of the other games so I wouldn't know size differences.
I have been working on fixing the script though. So far I have it in the menu and I can load the ski file and read it. I still need to get Blender make the model and attach materials and textures.
Aww but 3D modeling is fun. Changing the colors is just opening the dds texture in photoshop/gimp and repainting it. It shouldn't be too hard.
This might help you for gfx files. It tells you how to convert colors so you can change the color of the gfx.
http://forum.ragezone.com/f755/gfx-colors-numbers-667113/#post5693996
Then you just change the color attribute in the file.
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There also isnt any video guides or 1,2,3 guides as its not that simple. The are many different ways you can create model in a 3d modelling app and everyone has their own preference. All the different methods can be found on 3d sites and forums.