Here's what I did from the beginning:
1) Download the OTA package and the 1.65
update zip onto my Nexus 7 (2012)
2) Restored all files on the /system partition to their stock versions (I had a custom boot animation and the AOSP Browser installed.)
3) Go into SuperSU and hit ''Full unroot."
4) Boot into custom recovery (I use CWM, but I guess any custom recovery will work.)
5) Flash OTA package.
6) Flash SuperSU 1.65
7) Boot up the tablet into its shiny new OS.
8) Install SuperSU from the play store, as it won't show up in the app drawer.
9) Run SuperSU and hit yes to update su (normal method.)
10) Quickly go into settings and hit "install SuperSU to system" before it crashes (if it crashes just try again.)
11) When the tablet reboots (reboot manually if it doesn't) repeat step 10 once.
12) Hope that it works, if it doesn't, run SuperSU, try either reinstall, switch superuser app, or full unroot and start over at step 6.
If you already have the OTA applied, just boot into recovery and start at step 6.