sorry if i mislead you,been a long time since i saw the vids,i must have thinked another thing,guess my memory's a little rusty.
did you test the mileena_e mod i sent you(well,rather the tutorial to recreate it)? i was wondering if the pc version of mileena_e has the same backface culling as the ps3 one.
folks,while i do know that the transparent holes can be due to missing textures,as we've seen,there are also cases of backface culling,to the point where it's getting annoying(for example,and excuse the overall perversity of the following example,mileena_e has a full body texture,and the bandages are layed on top of her body,removing the bandages causes transparent holes(except for some parts,very minor ones at that) where they shouldn't be. i think JC's bandages are also like this IIRC. it seems if you can't see a part of the skin when there's something on top of it(even if the texture of that part of the skin exists) it just does backface culling,but it could be also be determined specifically by the game(who knows,maybe even by the textures) main reason why i say this is because,when i tested the bandage removal of mileena_e,i noticed a part on her back(the largest one) has a slight part that shows skin even though unmodded,it's completely bandaged and you can't see anything,which is really bizarre considering it's completely covered up,yet a slight part shows up without backface culling. we should start looking at this,it may not be determined by the meshes,maybe by one of the textures or something MIC related.
It seems to be a combination of texture mapping (or lack thereof), backface culling, and poly intersection that are causing the issues we are having. Goro's shoulder pad, for example, removes just fine... this is because it sits on top of the leather strap and thus it doesn't touch the skin. The wrist and leg armor intersects the skin though and I think that is the issue. This is why masks, hats, glasses, ect can be easily removed along with hanging cloth and ect while other stuff can't.