Here's an "empty" version of the OTA .zip file that you can use with OTA Verifier:
View attachment 443-n7-naksai-OTA-empty.zip
I basically removed all of the files except for the files in the
META-INF\com\google\android structure (i.e., the signing files and the updater-script and update-binary, of which the
updater-script file is the only useful file to
OTA Verifier.
Note: this file is NOT useful for flashing since there are no resource / payload files present for it to use for it's commands.
I'm guessing you do have some files that don't match what the OTA expects which accounts for your initial installation failure...
Also if you have the official ota will it flash through twrp?
will you or someone else eventually post it somewhere?
like can you just clear cache dalvik cache with twrp and flash ota?
Would save time waiting for it to showup and download the conventional way.
Well, I've got the 2012 (first gen) grouper/nakasi wi-fi version of the OTA...I was about to post it on my dropbox for you, but I see that it's also available here:
http://android.clients.google.com/packages/ota/google_nakasi/ce921efc1fa9197e9b336ce3f89cbfa2275ea4bb.signed-nakasi-KTU84L-from-KOT49H.ce921efc.zip
courtesy of this G+ post:
https://plus.google.com/+DroidLife/posts/bjbNvcra5XJ
In reviewing the updater-script file, I don't see any checks that tests the currently installed recovery, so my thought is that it should flash from a custom recovery okay, but I haven't tried so I can't say 100% for sure (if you're brave enough, you could always just make a Nandroid backup, squirrel it off of your device to a safe place, and try it--knowing you'll be able to restore the Nandroid and/or flash the factory image).
Or, if you have re-rooted, and
have verified that you've resolved any issues pointed-out by OTA Verifier, you could re-flash the stock N7 recovery using either manually or using my Android Root Toolkit app. Then you should be able to simply copy the above full OTA file (ce921efc1fa9197e9b336ce3f89cbfa2275ea4bb.signed-nakasi-KTU84L-from-KOT49H.ce921efc.zip) to your /cache folder and reboot--that should simulate receiving the OTA.
Would save time waiting for it to showup and download the conventional way.
Would that method leave all the data and installed apps intact?
Yes.