For my unlocked and rooted Nexus mobile, I just grabbed the 4.1.2 factory image, edited the flash batch file to remove the -w flag and removed userdata.img from the package and applied the update. The instructions are easy to follow and all over xda.
"For update to 4.1.2 without losing any userdata or Apps do following:
1. Download "takju-jzo54k-factory-92830c0b.tgz" and unpack it.
2. Edit "flash-all.bat" with Text Editor and remove "-w" from it.
3. Delete "userdata.img" from "image-takju-jzo54k.zip".
4. Put phone in fastboot modus and then run "flash-all.bat"."
Running 4.1.2 perfectly fine with no personal data lost.