The install procedure says to restore InstallESD.dmg to a partition. This turned out to be tricky. Restore from the dmg fails, due to "invalid parameters" .  Mounting the dmg, and restoring with the mounted version works. But then the partition and filesystem verification can fail, which prevent installation. So some tips:

• Create a separate Install Partition
• Ensure that there are no more than 4 total partitions on the drive
• Install Partition should be at least 8gb
• Ensure that the install partition is the second partition
• Ensure the success of  "verify disk" on the whole disk, and "verify disk" for each partition/volume.

OSX did not like the HFS+ partitions that I created with gparted. diskpart complained that there was not enough "loader space" no matter what I did. So within OSX, (on the virtual Mac) I erased all but the invisible ESP partition, and created an install and an OSX partition on the Mac drive. I restored InstallESD to the install partition, and re-installed Clover 1946 to the OS partition. All tests show good. I expect I must reinstall Clover yet again on the OS partition, go get the correct kexts and DSDT.aml.

Now to try booting again.

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!

Plugging in the USB drive did something to the UD7's nvram, now I can see Clover every boot, evrn with no USB present. However, Clover is not reading the config files. I guess it may be the X79-UD7 config dir I created. my blind trial and error. I am annoyed that I compiled a debug-by-default version of Clover, but still no log files. I have NEVER seen a Clover log file.
On the plus side, I seem to be able to boot Windows from Clover.

I hate computers.
At LEAST three full workdays of effort attempting to get Clover to start on the UD7, with no results. Almost by accident, I started the UD7 with an iATKOS ML3 bootable USB drive. That drive has Clover 1850. Sure enough, Clover starts fine from the USB. but Its what happend next that is so odd.
I unplug the USB, reboot, and go to the kitchen to get a drink. I come back, and there it is. Clover has finally booted from the Mac drive. And unlike on the the VM, Clover  is correctly reading the confing.plist.
I had to hard reset to boot windows again, becuse the Clover option to boot windows did not work. Still good news, at least I know it is possible to get clover to run on the UD7. Now I need to discover  WHY it needs the USB drive to boot from the SATA Mac drive.

CRAZY!

Turns out that a VirtualBox EFI virtual machine CAN boot Clover with my Mac drive. I don't know what that means. And it is certainly a broken, clover, with no config file read correctly. I think this because the theme is "embedded" instead of any of the ones I have picked, and none of the other options I set in the condif work either.
It is so frustrating that Clover USED to work fine on the UD7. THIS NOT SUPPOSED TO BE THE HARD PART.

I still hve not opened the case yet, but I think it is a GPT/parition/filesystem/EFI data problem, not a Motherboard/Firmware problem. The evidence is that when I disconnect all the other drives, I see the UEFI: label for the Mac drive, and can selet it for boot. but then I get the no-media message instead of Clover.

Using the downloaded Clover r1943 did not work, so I am going to build a new custom Clover 1945. I don't expect that to make the ESP on the Mac drive be recognized either, but opening the case is so much work, ANY software solution is worth a try.

It is very annoying to take such a big step backward, considering that I previously had Clover running successfully.

This is possibly an undocumented limitation of the UD7, or the Chipset, or the controller, where only some ports of some SATA controllers are recognized as bootable UEFI devices. However, the Mac drive is on the same SATA controller as the Windows boot drive, and disconnecting the Windows drive does not help.

The Mac drive is currently on Bus Number 5, Target Id 0 Lun 0. The “Friendly name” is ATA ST1000DM003-1CH1 SCSI Disk Device. The SATA controller is Intel C600 Series Chipset SATA RAID Controller.