Rigging process is not unclear, its just different with every model but there's a lot of guessing involved when it's your first try.
If there's a bone near the verts there's a good chance you'll assign weights from it, the torso will most likely use the lower lumbar, upper & thoracic, because that is how it will bend in the game...its the same principle in real life.
No, you dont have to apply the 50/50 method everytime, what you need to do is weight the character first and not worry about the caps. The caps should be done later because they will behave like their parent mesh. You can leave them in the scene, you will temporarily delete them when exporting. Once you are happy with the animation then you can throw them into the mix.
To rotate the bones, use the rotate tool at the top (near the move and scale tool), you have to be careful when doing this, you need to set the bones back to their original state or it'll mess the basepose. What you do is turn on angle snap (press a) and it should rotate in increments of 5 degrees so if you mess up you will be able to rotate back easily since it wont be a random rotation.
I cant find a "torso_cape" bone in the max scene you provided...or meshes, there's only tags called "bolt_torso_cap" which arent the same thing. The extracted JA skeleton from Agustin aka "Corto", did in fact have 2 extra bones for weighting alora's "tentacles" or whatever you call those. They were simply small extensions of the upper leg bone so they were not a major improvement for capes or robes.
You're welcome, i guess i should have made the tutorial with audio, it would have made it a whole lot easier