shoulders placement

I guess the skin modifier wont get you perfect results, you fiddle the best you can but in the end I think you're going to have to do some manual adjustments after you apply it. But while you have the skin modifier you could try on a vert doing Control + A to adjust the radius and that helps a ton. Also try moving the root around. So you select a vert and on the modifier you mark it as root and that also mves things around and helps. Try that on different verts. Hope that helps.