If you flash a custom ROM to your Nexus 7, you will not be able to flash OTA updates. Also, your warranty will be void. These are two scenarios that come to my mind why a user might want to restore the stock recovery. Here is how you do it.
1: Before you proceed, I assume you do have any update ZIP files on the root of your storage. I also assume you have the USB drivers installed. If not, install them from here.
2: Download the appropriate 126.96.36.199 file for your device from here:
3: Extract files from within zip
4: Extract files again from the extracted zip
5: Copy extracted "blob" file to root of folder of the removable Micro SD card or some other folder
6: Through ADB shell or Terminal Emulator, run the following: (May take from 5 to 20 minutes)
su dd if=/Removable/MicroSD/blob of=/dev/block/mmcblk0p4
If copying the "blob" file to the SD card in the keyboard dock, use: dd if=/Removable/SD/blob of=/dev/block/mmcblk0p4
If copying it to the internal memory, use:
dd if=/sdcard/blob of=/dev/block/mmcblk0p4
7: Reboot only if the following is displayed (exact numbers may be different): 1068769+1 records in 1068769+1 records out 547210197 bytes transferred in 153.991 secs (3553520 bytes/sec)
Update process will automatically launch
8: Once booted up, root device by using debugfs root here
9: Do not make any other changes to build.prop or the /system directory
10: Download the appropriate dlpkgfile. The US version of the update can be downloaded here.
11: Use root explorer to copy "dlpkgfile" into /cache/ directory. Alternatively you could save the "dlpkgfile" in a microSD then open up a adb shell session.
su cat /Removable/MicroSD/dlpkgfile > /cache/dlpkgfile
12: Create the file called "command" under /cache/recovery/ directory.
13: Write this statement in the file /cache/recovery/command
14: Finally reboot into recovery kernel by shutting down first, then press and hold "Volume down" + "Power" once it vibrates release "Power" keep holding "Volume down" until there are some text shown on the boot logo screen. Then press "Volume up" within 5 seconds after releasing "Volume down". The update process should start… wait for it to complete. (This will take a little while, as the dalvik-cache will be rebuilt and your camera firmware will be updated. Once it completes, you should have the updated firmware installed on your tablet.
Also check out Nexus 7 stock rom postrelated queries: dlpkgfile, nexus 7 restore original recovery, restore stock rom using custom recovery on nexus 7