You should have both Scene Layers 1 and 3 selected so both layers affect each other. Your render layers can stay as is.
Also, you are using Layer 3 to mask out Layer 1, but because Layer 3 contains objects in front and behind the character on Layer 1 it's masking out the character completely.
You'll probably need to need put the elements behind the character (floor, etc.) on a different layer.
I'm getting something like this for the Shadows>Shadow pass.
Also, I noticed you're rendering out to PNG file without using the compositor. Doing it this way will just give you your main Combined pass. You'll need to render to a MultiLayer EXR (renders all passes into one file per frame), OR you'll have to set up File Output nodes in the compositor to render out separate PNG image sequences for the additional render passes you need.