Now that the firmware update appears to have settled down I added the new settings to the D3 spreadsheet.
Note that the description of the firmware update states that default for Vignette control is Normal and default for Focus point brightness is Normal. However, after I upload the updated firmware the camera was set to Vignette control Off and Focus point brightness Low.
The spreadsheet still needs some work. In particular, I don't have a wireless transmitter or a GPS, so settings for those menu items still have to be defined.