You need stock recovery to install an OTA update. To get stock recovery back, you repeat the same steps that you used to install Clockwork. do the following:
1) download
stock-recovery.img, extract the file inside, place the file in the nexus7 folder (C:\nexus7)
2) reboot into bootloader (power off, hold vol down+power), plug in tablet to PC via USB
3) open Windows command prompt (cmd), navigate to the nexus7 folder in the command prompt (cd c:\nexus7)
4) in command prompt, type "fastboot devices" to make sure your tablet is connected properly, then type "fastboot flash recovery stock-recovery.img" to get stock recovery back, then reboot the bootloader by typing "fastboot reboot-bootloader" to finish installation
5) using the volume keys, go to "Recovery mode" on the bootloader screen and press power to select it
6) you should now see stock recovery, which is a little Android laying down with an exclamation point over him. if you see this, then you're ready to apply the OTA update. reboot and apply the 4.1.1 update as normal.
7) after you apply the OTA update, if you want Clockwork back repeat the above steps but instead of using "stock-reocvery.img" use "clockwork.img" from the video (it should already be in your nexus7 folder).
if you lose root access after the OTA update, check to see if SuperSU is still in your app list. if it is, open it and tap yes when it asks to install binaries, then you'll have root access back.