Noob Nexus Root How To IMHO
I rooted for the first time this week and I thought there were some things missing in the instructions I followed. Here is my Nexus root method for noobs:
1. Install
Wugfresh toolkit and follow the instructions for installing drivers.
Wugfresh may freeze at any point in this process - I had to restart it a few times, no ill effects, so don’t sweat it.
2. If any of your apps allow you to perform a backup, do so.
3. Backup APN so you don’t lose your wifi passwords.
4. I think backing up contacts is redundant - your choice.
5. If you have apps on your screen(s), take a screenshot of them.
6. Backup data / media.
7. Run the backup to Create Android Backup file. You can do system apps + data if you are going to backup again after root. The last backup before installing ROM should not include data.
8. Unlock and Root.
9. Do a nandroid backup - in case there is a problem with the ROM install, you can get back to a rooted phone with your stock ROM.
10. Copy the ROM (name it update.zip) to your download folder on the phone - it will be there after you wipe again.
11. Launch Advanced Utilities
12. Flash zips
13. After phone boots into your custom ROM, restore from Steps 3 - 6.
14. Reboot - everything aside from you old screens should be back.
15. Change Wugfresh to your current setup (custom ROM)
16. Do another nandroid backup - if you do any further tinkering that screws things up - you can get back to this successful custom ROM.
I hope this helps, enjoy.

LTE Galaxy Nexus
Latest Shiny ROM / tiny kernel
check init.d settings script -
checkinit