I think this is what makes it so tough....it is a mix of everything you listed and it will vary person to person. I would always look at the bottom half first. Almost every pitcher I see when I do go to games....be it youth games, high school games or mens league games....swing their front leg open. Call it opening up or whatever you want. I call it early rotation....that early rotation with bottom half makes it tough to stay closed and create hip/shoulder separation.
Just my humble opinion, but, until the lower half is "fixed"....meaning a thrower is getting energy moving down the mound in way that allows for balance and a late, explosive hip rotation, the shoulders are probably going to open with the bottom half. A "one piece" delivery if you will.
So, to me, it starts with the lower half and moves up.