Your method is good when you work on original pictures, not on remodelised screens. Sometimes there are gaps between what the graphic designer manages to do and the original picture. Some elements are not exactly in the same position. It's why you must slice by yourself when you have stuffes like chairs or ramps (all what the characters pass behind). It's also why it takes me some hours to have a good slicing...
You also can't take the original layer when you have a diagonal line, because you'll have a big aliasing effect. The original picture have less details, so all the diagonals will have a staircase effect, but on the high definition image, the line will be straight.
Layering is not an easy part of the job...Whoever wants to do it will have to be very precise and will have to cut back almost everything without following the original layout.
I hope my explanations are clear, I'm french and it's not easy to find the good words !
It doesn't matter if you don't have the layers anymore, I saied to Faulked I'll make the layering, so I planned to do it anyway