Update Galaxy Nexus from 4.2.2 to 4.3 while keeping files and root
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.