How I updated my rooted nexus 5 with a custom kernel to kitkat 4.4.1

1. Download the 4.4.1 image (7ed504f678cea49ecf0974e8cd956e2974e3f943.signed-hammerhead-KOT49E-from-KRT16M.7ed504f6.zip)
2. Download the stock image (hammerhead-krt16m-factory-bd9c39de.tgz).
3. Copy the updated image to the phone
   
   $ adb push ~/Downloads/7ed504f678cea49ecf0974e8cd956e2974e3f943.signed-hammerhead-KOT49E-from-KRT16M.7ed504f6.zip  /mnt/sdcard/
   
   
4. Reboot into fastboot (power and volume down when booting).
5. Extract the stock image.
   
   $ tar zxvf hammerhead-krt16m-factory-bd9c39de.tgz
   
   
6. Unzip the image
   
   $ unzip image-hammerhead-krt16m.zip
   
   
7. Flash the boot img
   
   $ fastboot flash boot boot.img
   
   
8. Reboot into bootloader
   
   $ fastboot reboot-bootloader
   
   
9. Flash the system img.
   
   $ fastboot flash system system.img
   
   
10. Go into recovery (TWRP for me) and flash the 4.4.1 update copied over earlier. 
11. Flash custom kernel on sdcard.
12. Let twrp install supersu and reboot.
13. Not rooted - download the latest twrp (openrecovery-twrp-2.6.3.4-hammerhead.img)
14. Reboot into fastboot mode again.
15. Flash the twrp image
    
    $ openrecovery-twrp-2.6.3.4-hammerhead.img
    
    
16. Boot into recovery mode.
17. Download latest supersu (UPDATE-SuperSU-v1.80.zip)
18. Copy supersu over to card.
    
    $ adb push UPDATE-SuperSU-v1.80.zip  /sdcard/update-supersu-v1.80.zip
    
    
19. Install it from TWRP.
20. Done.