I don't know much about rooting, so I thought I'd post the steps I followed to update from a rooted (but stock kernel) 4.0.2 to 4.0.4 for anyone else who is also not that experienced with this sort of thing. Note: I had already followed this page to root 4.0.2. Downloaded the LTE 4.0.2-4.0.4 update from here onto the phone. Rebooted into recovery mode and chose install zip from SD card (12f767e7a5d0.signed-mysid-IMM76K-from-ICL53F.12f767e7.zip). Rebooted normally and let OS run another update. Rebooted into fastboot and connected via USB. On OSX, went to ~/Downloads/GalaxyNexusRootNew and ran ./fastboot-mac flash recovery optimus_prime-touch-v18.104.22.168-6-toro-VERIZON.img (had been previously downloaded). Those of you running Windows or Linux, see step 8 from the original instructions for your syntax. Rebooted into recovery mode, chose install zip from SD card (CWM-SuperSU-v0.87.zip). Rebooted normally and updated SuperSU.