[Nexus 7 General] ShadowOf:
My Nexus 7 [WiFi] was rooted on 4.2.2, unlocked bootloader, but stock rom, stock system (as far as I remember). I couldn't find a walkthrough so I'll make one with my experience.

I found a walkthrough for Nexus 4, so minus the download packages and the radio img it was the same. This worked for me on my mac, I hope this helps you.

In the end I didn't lose any data, still have unlocked bootloader and rooted with CWM Touch Recovery & SuperSU

(you can replace with TWRP)

Directions

("XXX/" = file path to platform-tools folder)

1. You must have Android SDK installed. Download it here: http://developer.android.com/sdk/index.html.

2. UNZIP and you will see a bunch of folders. The one we are interested in is the subfolder "platform-tools". You may copy it to an easier location if you want.

3. Download the factory image 4.3 for your Nexus 7: https://developers.google.com/android/nexus/images#nakasi (WARNING: Download the correct image for YOUR device, Nexus 7 WiFi vs Mobile)

4. Unzip the 4.3 image file you downloaded and copy all its content to your "platform-tools" folder (where adb and fastboot are).

5. Plug your Nexus 7 into your computer with USB debugging (activate it in "About Phone" and touch "Build number" 6 times, it will activate a "Developer Options" menu where you will be able to activate "USB debugging")

6. Verify ADB is working. Open a terminal and type "XXX/adb devices"

7. Reboot your device into fastboot mode: type in terminal "XXX/adb reboot-bootloader"

8. Type:

"XXX/fastboot flash bootloader XXX/bootloader-grouper-4.23.img" (img name depends on your build)

9. If you have "WiFi Only" skip to step 10; for Mobile/GSM flash radio type:

"XXX/fastboot reboot-bootloader"

"XXX/fastboot flash radio XXX/radio-tilapia-1231_0.18.0_0409.img" (img name depends on your build)

10. Type:

"XXX/fastboot reboot-bootloader"

"XXX/fastboot update XXX/image-nakasi-jwr66v.zip" (zip name depends on your build)

It will then reboot (

takes a while

) and then you will be in Android 4.3 with all your data preserved.

Then if you want to root:

1. On your computer, download CWM or TWRP recovery from here: CWM Dwnld or TWRP Dwnld (WARNING: Download the correct image for YOUR device, Nexus 7 WiFi vs Mobile)

2. Place the image file you downloaded in your "platform-tools" folder (where adb and fastboot are).

3. Connect your Nexus 7 (debug mode) and put it in fastboot mode (step 7 above)

4. In the terminal type: "XXX/fastboot flash recovery XXX/FILENAME.img (replace FILENAME by the file name of the CWM/TWRP file you just downloaded)

5. Reboot your device

6. Download directly to your device the most recent SuperSU file: http://download.chainfire.eu/supersu

7. Shut down your device and boot it into recovery mode (Once off, push vol- and power together). Choose recovery mode with vol-, then power to select

8. Once you are in recovery mode select "Install ZIP", look for SuperSU file you just downloaded and follow instructions to flash the zip file.

9. Reboot your device

That's it!

Thanks to jipi: http://xdaforums.com/showthread.php?t=2377691

Already updated to 4.3 and have an OTA notificaion? (JWR66Y from JWR66V)

Here is the easy, no-nonsense way of installing the OTA on Nexus 7, no PC or cables needed.

NOTE: This will ONLY work on totally stock but rooted. If you changed anything else at all, then you will need to load stock to get the OTA patch to work.

1. Download the OTA file to your device. You can find a link in this thread: http://xdaforums.com/showthread.php?t=1745781 (WARNING: Download the correct image for YOUR device, Nexus 7 WiFi vs Mobile)

2. Download directly to your device the most recent SuperSU file: http://download.chainfire.eu/supersu

3. Open the SuperSU app and select Full Unroot.

4. Shut down your device and boot it into recovery mode (Once off, push vol- and power together). Choose recovery mode with vol-, then power to select.

5. Once you are in recovery mode select "Install ZIP", look for OTA file you just downloaded and follow instructions to flash the zip file.

6. WITHOUT rebooting, install the SuperSU file again using "Install ZIP".

7. Reboot your device

(8/24/13) Update: Added directions to updating to the latest build, avoiding the OTA and loosing root.

(8/15/13) Update: Updated link to factory image to better show options for download, was going straight to the 4.3 WiFi link. Added a warning to the factory image and CWM/TWRP download links, to verify you are downloading the image for YOUR device. Good luck and happy flashing.