Jack,
I am sure you can find (and you have found some) guidance from others on how they set up the camera. However, I do not believe there is a sensible copy-and-be-happy approach. You need to figure out how to set it up for your need.
Personally I am not even close to using the camera to its fullest potential and I only master a minor part of its functional capabilities. My approach has been to think critically on what I need and what suits me. The most important being:
I use the AF-On button to activate one-shot in servo mode and not for BB focus.
I select number of AF points with the AF point selector (activate) and the front wheel (select).
I change ISO settings with the set button(activate) and the back wheel (select).
All other buttons are kept with their default functionality.
When it comes to all the internal settings, I do not believe there is a one package fits all option. You must spend time trying to understand what they do. In principle, you do nothing wrong by leaving them in their default position and then do them one by one as your experience grows.
One thing I am missing or have not been able to figure out, is how I can dial in exposure compensation in manual mode, without taking my eye away from the viewer. Currently I have to look at the display and it annoys me. If someone know if/how this can be done, I'd be happy.
As a sidenote, my camera fell on rocks the other day, so the mirror housing is damaged and the sensor is out of position ...