[Nexus 6 Q&A, Help & Troubleshooting] GuardianUSMC:
Alright, good news, it worked and thank you for pointing to the resource that allowed me to figure out why I was getting the partition errors, now I know.

I modified the batch file as follows:

PATH=%PATH%;"%SYSTEMROOT%\System32"
adb reboot bootloader

fastboot flash bootloader bootloader-shamu-moto-apq8084-71.08.img
fastboot reboot-bootloader
fastboot flash radio radio-shamu-d4.0-9625-02.95.img
fastboot reboot-bootloader

fastboot flash system system.img
fastboot flash userdata userdata.img
fastboot flash boot boot.img
fastboot flash recovery recovery.img
fastboot erase cache
fastboot flash cache cache.img
fastboot reboot-bootloader

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

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

it went through the whole process and here is the resulting output:

C:\Users\Major\Desktop\shamu-lmy47i>flash-all.bat
< waiting for device >
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 [ 0.508s]
finished. total time: 0.632s
rebooting into bootloader...
OKAY [ 0.002s]
finished. total time: 0.002s
< waiting for device >
target reported max download size of 536870912 bytes
sending 'radio' (85422 KB)...
OKAY [ 2.722s]
writing 'radio'...
(bootloader) flashing modem ...
(bootloader) flashing mdm1m9kefs1 ...
(bootloader) flashing mdm1m9kefs2 ...
(bootloader) flashing mdm1m9kefs3 ...
(bootloader) flashing versions ...
OKAY [ 1.110s]
finished. total time: 3.834s
rebooting into bootloader...
OKAY [ 0.002s]
finished. total time: 0.003s
< waiting for device >
target reported max download size of 536870912 bytes
sending sparse 'system' (522196 KB)...
OKAY [ 22.442s]
writing 'system'...
OKAY [ 7.691s]
sending sparse 'system' (510114 KB)...
OKAY [ 21.723s]
writing 'system'...
OKAY [ 6.674s]
sending sparse 'system' (514997 KB)...
OKAY [ 21.128s]
writing 'system'...
OKAY [ 7.778s]
sending sparse 'system' (189177 KB)...
OKAY [ 7.652s]
writing 'system'...
OKAY [ 2.328s]
finished. total time: 97.428s
target reported max download size of 536870912 bytes
erasing 'userdata'...
OKAY [ 11.844s]
sending 'userdata' (138868 KB)...
OKAY [ 4.518s]
writing 'userdata'...
OKAY [ 1.949s]
finished. total time: 18.315s
target reported max download size of 536870912 bytes
sending 'boot' (7681 KB)...
OKAY [ 0.247s]
writing 'boot'...
OKAY [ 0.110s]
finished. total time: 0.359s
target reported max download size of 536870912 bytes
sending 'recovery' (8273 KB)...
OKAY [ 0.266s]
writing 'recovery'...
OKAY [ 0.116s]
finished. total time: 0.384s
******** Did you mean to fastboot format this partition?
erasing 'cache'...
OKAY [ 0.045s]
finished. total time: 0.046s
target reported max download size of 536870912 bytes
erasing 'cache'...
OKAY [ 0.013s]
sending 'cache' (6248 KB)...
OKAY [ 0.204s]
writing 'cache'...
OKAY [ 0.097s]
finished. total time: 0.318s
rebooting into bootloader...
OKAY [ 0.002s]
finished. total time: 0.003s
< waiting for device >
downloading 'boot.img'...
OKAY [ 0.399s]
booting...
OKAY [ 0.035s]
finished. total time: 0.436s

Thank you for everyone's input and assistance here, you rock.