[Nexus 6 Q&A, Help & Troubleshooting] GuardianUSMC:
Just to share, I am trying to flash the factory image that I mentioned in my original post, so I won't repost it. Here is what did so far to no avail, so any assistance would be greatly appreciated:

I issue the command adb reboot bootloader and it successful reboots the phone into the bootloader

Extracting the folder shamu-lmy47i containing the following files:

bootloader-shamu-moto-apq8084-71.08.img

flash-all.bat

flash-all.sh

flash-base.sh

image-shamu-lmy47i.zip

radio-shamu-d4.0-9625-02.95.img

Opening the batch file you see the following (I have removed the copyright header for sake of brevity)

PATH=%PATH%;"%SYSTEMROOT%\System32"
fastboot flash bootloader bootloader-shamu-moto-apq8084-71.08.img
fastboot reboot-bootloader
ping -n 5 127.0.0.1 >nul
fastboot flash radio radio-shamu-d4.0-9625-02.95.img
fastboot reboot-bootloader
ping -n 5 127.0.0.1 >nul
fastboot -w update image-shamu-lmy47i.zip

echo Press any key to exit...
pause >nul
exit

Since the only thing I want to add to this is root, I add this after the image update:

fastboot boot CF-Auto-Root-shamu-shamu-nexus6.img

So we let it rip and this is the resulting output:

C:\Users\Major\Desktop\shamu-lmy47i>flash-all.bat
target reported max download size of 536870912 bytes
sending 'bootloader' (3807 KB)...
OKAY [ 0.123s]
writing 'bootloader'...
(bootloader) flashing partition ...
(bootloader) This may take a few seconds if a
(bootloader) different partition table is being
(bootloader) flashed since we need to backup
(bootloader) and restore a few partitions
(bootloader) Flashing primary GPT image...
(bootloader) Flashing backup GPT image...
(bootloader) flashing aboot ...
(bootloader) flashing sbl1 ...
(bootloader) flashing rpm ...
(bootloader) flashing tz ...
(bootloader) flashing sdi ...
(bootloader) flashing logo ...
OKAY [ 0.548s]
finished. total time: 0.674s
rebooting into bootloader...
OKAY [ 0.002s]
finished. total time: 0.003s
target reported max download size of 536870912 bytes
sending 'radio' (85422 KB)...
OKAY [ 2.720s]
writing 'radio'...
(bootloader) flashing modem ...
(bootloader) flashing mdm1m9kefs1 ...
(bootloader) flashing mdm1m9kefs2 ...
(bootloader) flashing mdm1m9kefs3 ...
(bootloader) flashing versions ...
OKAY [ 1.102s]
finished. total time: 3.824s
rebooting into bootloader...
OKAY [ 0.002s]
finished. total time: 0.003s
target reported max download size of 536870912 bytes
archive does not contain 'boot.sig'
archive does not contain 'recovery.sig'
failed to allocate 1778160592 bytes
error: update package missing system.img
downloading 'boot.img'...
OKAY [ 0.393s]
booting...
OKAY [ 0.024s]
finished. total time: 0.419s
Press any key to exit...

As we can see, bootloader image flashes just fine

The radio image flashes just fine

System image on the other hand does not update complaining about missing .sig files:

The files inside this system zip are:

android-info.txt

boot.img

cache.img

recovery.img

system.img

userdata.img

Ironically the SuperSU image flashes just fine and reboots the phone

I am frustrated by the fact that the system image update step fails and nothing out there explains why? I have even tried to extract each of those images from the zip file and flashing them individually using the fastboot flashall but getting the same error as well as other errors.

Can anyone lend an assist on this and help me figure out how to overcome that hurdle PLEASE?