[Nexus 5 Q&A, Help & Troubleshooting] bourne-nolonger:
Sorry for the late reply on this.

I got around to doing the steps above.

Unfortunately I am still stuck on the boot animation screen.

Here is the output from the commands I ran

C:\Temp\hammerhead-mmb29s-factory-6bfcdfa4\hammerhead-mmb29s>flash-all.bat
target reported max download size of 1073741824 bytes
sending 'bootloader' (3120 KB)...
OKAY [ 0.297s]
writing 'bootloader'...
OKAY [ 0.500s]
finished. total time: 0.797s
rebooting into bootloader...
OKAY [ 0.063s]
finished. total time: 0.078s
target reported max download size of 1073741824 bytes
sending 'radio' (45425 KB)...
OKAY [ 1.540s]
writing 'radio'...
OKAY [ 3.125s]
finished. total time: 4.665s
rebooting into bootloader...
OKAY [ 0.063s]
finished. total time: 0.063s
target reported max download size of 1073741824 bytes
archive does not contain 'boot.sig'
archive does not contain 'recovery.sig'
archive does not contain 'system.sig'
archive does not contain 'vendor.img'
Creating filesystem with parameters:
Size: 13725835264
Block size: 4096
Blocks per group: 32768
Inodes per group: 8144
Inode size: 256
Journal blocks: 32768
Label:
Blocks: 3351034
Block groups: 103
Reserved block group size: 823
Created filesystem with 11/838832 inodes and 93654/3351034 blocks
Creating filesystem with parameters:
Size: 734003200
Block size: 4096
Blocks per group: 32768
Inodes per group: 7472
Inode size: 256
Journal blocks: 2800
Label:
Blocks: 179200
Block groups: 6
Reserved block group size: 47
Created filesystem with 11/44832 inodes and 5813/179200 blocks
--------------------------------------------
Bootloader Version...: HHZ12k
Baseband Version.....: M8974A-2.0.50.2.28
Serial Number........:
--------------------------------------------
checking product...
OKAY [ 0.094s]
checking version-bootloader...
OKAY [ 0.109s]
checking version-baseband...
OKAY [ 0.094s]
sending 'boot' (9154 KB)...
OKAY [ 0.500s]
writing 'boot'...
OKAY [ 0.781s]
sending 'recovery' (10012 KB)...
OKAY [ 0.562s]
writing 'recovery'...
OKAY [ 0.828s]
erasing 'system'...
OKAY [ 1.297s]
sending 'system' (1020413 KB)...
OKAY [ 32.163s]
writing 'system'...
OKAY [ 69.508s]
erasing 'userdata'...
OKAY [ 8.326s]
sending 'userdata' (137318 KB)...
OKAY [ 4.500s]
writing 'userdata'...
OKAY [ 9.138s]
erasing 'cache'...
OKAY [ 0.672s]
sending 'cache' (13348 KB)...
OKAY [ 0.625s]
writing 'cache'...
OKAY [ 1.078s]
rebooting...

finished. total time: 130.775s
Press any key to exit...

////// -------- AFTER COMPLETE POWER OFF AND REBOOT -------- \\\\\\\\

C:\Temp\hammerhead-mmb29s-factory-6bfcdfa4\hammerhead-mmb29s\image-hammerhead-mmb29s>fastboot erase cache
******** Did you mean to fastboot format this partition?
erasing 'cache'...
OKAY [ 0.625s]
finished. total time: 0.641s

C:\Temp\hammerhead-mmb29s-factory-6bfcdfa4\hammerhead-mmb29s\image-hammerhead-mmb29s>fastboot erase userdata
******** Did you mean to fastboot format this partition?
erasing 'userdata'...
OKAY [ 8.384s]
finished. total time: 8.399s

C:\Temp\hammerhead-mmb29s-factory-6bfcdfa4\hammerhead-mmb29s\image-hammerhead-mmb29s>fastboot flash userdata userdata.img
target reported max download size of 1073741824 bytes
erasing 'userdata'...
OKAY [ 8.220s]
sending 'userdata' (137318 KB)...
OKAY [ 4.516s]
writing 'userdata'...
OKAY [ 9.156s]
finished. total time: 21.892s

Everything seemed to go okay.

Does everything in the output above look okay?