Whooo.... I just looked at that spreadsheet after setting up my camera. That's very comprehensive. I use about 1/10 of that stuff!
Honestly for me, once the camera has a basic setup with my metadata, clock, and so forth, The only things I change are the focus points depending on my sport/subject, ISO, mode, and other basics. I don't fool with picture controls because I shoot RAW. I shoot in 5:4 crop mode because I sell 8x10s and 4x5. And now 16x20s I guess.
My primary slot will always be CF, Active-D lighting is on Auto (which will slow the camera down in frame rate).
Most other things I find to be just user preference, or game-time decisions. For the most part, these things are just glorified film cameras to me so I only tend to sweat the things that affect picture quality, exposure, and focus. All the convenience features I leave to the younger guys with more time than me to figure them out.
It is remarkable how similar everything is to the D7000. Not sure if that's good or bad. But one thing that absolutely pisses me off is that I can't set up my focus points or other settings without a lens attached. None of my cameras are stored with lenses on them, so before a shoot, I have to put a lens on the thing just to prep. PITA.