You have selected vertex in subobject mode and its preventing the skin modifier to work. Select the hips and click on editable mesh, next click the vertex mode to turn off (when its off it wont be yellow).
You missed some of the verts and they have no weights assigned to them (between the legs and tip of the boots), dont forget to rotate bones to check for deformations and to see if you weighted all the verts. Always hit undo after rotating the bones to put them back into place.
What i usually do is turn on angle snap, this snaps the rotation to 5 degrees increments so if i accidentally cant set back the bone, i can easily rotate back because the rotations are not random. Pressing A will turn it on/off by default.
When you scaled the hands, the xforms were not reset and this could cause problems. Select the left arm and attach the left hand to it, repeat for right arm (pick arm first not the other way around!).
The cape should be named torso_cape because it's a non standard mesh and its parent mesh is the torso. l_handc should be called l_hand, same for the right hand and a few other meshes too.