Here is my experience with the update.
I am running the stock and rooted ROM (S-ON) with MiRaGe kernel (obviously unlocked bootloader). After rooting, I had done the following changes.
- disabled some of the apps in /system/app and replaced some of the google apps with the newer versions.
- due to MiRaGe kernel, the modules were different.
- disabled the boot sound and animation by renaming the related files
- I had 4ext recovery as well.
After receiving the OTA notification, I have reverted back to original recovery in fastboot. But I did not relock the bootloader. After reverting to original recovery, I rebooted and let the update proceed. In the first try, the update failed complaining about the renamed and different apps in /system. To see the errors, press volume up and power when you see the red triangle in the recovery screen. So I have restored them to original versions and names using ES File Explorer. I had the backups. Anticipating the same problem with modules, I have restored the original kernel modules as well. But didn't flash original boot.img. After these, I have retried the OTA and it completed with success.
You can open the OTA zip file and check the patches (files with .p extension) to see if you have modified any of the corresponding files in your stock ROM. In short, if you restore them, OTA completes without any need to relock bootloader or RUU restore. Again, the stock recovery is required.
The OTA process disables root but does not remove either Superuser.apk or su binary. You can root again by flashing the superuser package to regain root. TWRP 2.4.4 has the ability to restore root if it detects the apk and binary. It will ask if you want to enable root permission again.
As for custom kernels, MiRaGe kernel runs completely fine without any change with the latest OTA if you flash with Flash Image GUI. Everything works the same ... just faster

WiFi works even better due to updated drivers. One detail I have noticed is the WiFi MAC address was 001122334455. You can restore/change the WiFi MAC by editing /system/etc/calibration. Check the first line.
There is a new boot.img in the OTA. I have compared the kernel configs with the previous OTA (1.14). The only difference is that the kernel in the latest OTA comes without TZCOM option. I don't have it with MiRaGe kernel either. It wouldn't be a problem to have anyway, just an unnecessary kernel option to have.
Thank you for all the useful information here. I just wanted to contribute what I can.