I have a rooted GNex with stock kernel and stock ROM. Device is only rooted, CWM installed and unlocked bootloader.
I received the OTA update yesterday but haven't tried to apply it since I have a custom recovery installed. You should also know that I removed a file called recovery-from-boot.p to avoid the stock recovery from getting reflashed following the indications in this thread http://www.droidforums.net/forum/galaxy-nexus-development/189062-using-rom-manager-only-way-boot-into-clockwork-mod-recovery.html
I'd like to apply the OTA without losing my data and possibly not root. Losing root is not such a big problem but if you know a way of installing the 4.3 update from CWM without losing data then I'd be so thankful!