LOL... OTA's, why bother, this is a Nexus device you just flash the factory images. That being said, root is usually not the issue since Complete Unroot is an option in SuperSU, the real issue is any changes you make as root... if the recovery, /system partition, or /boot partition (ie. kernel) is modified the OTA won't go through anyway, rooted or not, so if you are rooted, make a change, then unroot, the OTA will fail anyway. Since it is always best to factory default after an upgrade, there is no advantage to an OTA on a Nexus device when you can just flash the factory images. Basically, any number of things you are doing will stop the OTA, you would essentially have to factory image, then take the OTA anyway, which is dumb. What I am trying to say here is you don't need to worry about this, IF another OTA comes for the N4, just flash the factory image and be G2G.
No, the process is too simple, you download the kernel zip and flash it in TWRP, reboot and install
HKM... if you need more information, look in the HellsCore kernel thread on XDA
here