MILESTONE!
Clover now starts every time.
Something, somehow, had smashed the top-level config.plist into binary garbage. I replaced it with a valid file. I also created a valid config.plist under:
EFI/CLOVER/OEM/X79-UD7/UEFI

And THAT config file, at long last, is read correctly. One way I know is because I set the theme to be different for all of the config plists.
So the ESP partition now has 7 config files that are almost exactly the same:

./CLOVER/OEM/SystemProductName/UEFI/config.plist
./CLOVER/OEM/SystemProductName/config.plist
./CLOVER/OEM/VirtualBox/UEFI/config.plist
./CLOVER/OEM/VirtualBox/config.plist
*./CLOVER/OEM/X79-UD7/UEFI/config.plist
./CLOVER/OEM/X79-UD7/config.plist
./CLOVER/config.plist

I am pretty sure that at least the top config file EFI/CLOVER/config.plist must be valid, or else none of the other configs are read. Again, for the GA-x79-UD7, the file "./CLOVER/OEM/X79-UD7/UEFI/config.plist" is the only one that is finally used. And Hurray, now that everything works, I have a debug file! :/

./CLOVER/misc/debug.log

0:100  0:000  Clover revision: 1946  running on To be filled by O.E.M.

0:100  0:000  ... with board X79-UD7

0:134  0:034  ConfigPlistPath: EFI\CLOVER\config.plist

0:140  0:006  Using OEM config.plist at path: EFI\CLOVER\OEM\X79-UD7\UEFI\config.plist

I duplicated the DSDT.aml and 10.8 kext files under the  CLOVER/OEM/X79-UD7/UEFI directory too.

Time to install, boot, and run the OSX 10.8 installer!