Aye... I see what you mean. The art of rigging tuts are great for specific techniques but what they don't do is tell you how they all work together - and I can see what you mean, particularly about the spine, as I recently had a look back at that myself.
To be honest... the whole grouping and connecting of these things once you are nearing the end of the rig, or have done the spine / leg /arm etc. is something that can't really be taught, as there are an million different rigging situations and solutions. I think it's something that just becomes more intuitive as you develop your rigging skills. That development comes from doing specific techniques that tuts like the art of rigging describe.
On to something a little more specific. Re. thi IK/FK switch. How have you set it up? Are you doing a 3 joint chain setup and, if so, are you using blendColo(u)r nodes or orient constraints?
Not sure what you've done with the shoulder controls... I'm guessing you've used some kind of position or orient constraint without maintaint the offset.
As for the box on the CoG... "I can't get it to do nothing"... hehe, what have you tried?
I'd best start working now, but if you can post the rig up here, maybe I can have a look around lunchtime or something.