Update Galaxy Nexus from 4.2.2 to 4.3 while keeping files and root 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!
You shouldn't lose any data by flashing the OTA file. You can flash the ota file (see AndroidPolice for info and where to download it from) and as long as you've not changed any system files it should apply ok. Simply select the "apply update from sdcard" option and select the update file. You will lose root but you can simply flash SuperSu (the only superuser app that works on 4.3 at the moment) which will "re-root" your device. If you get a prompt about disabling recovery flash, select "No" as the new SuperSu uses this part of getting root access.