Hey guys,
So I have the exact same problem, also with a 2012 N7 (unrooted, totally stock)... The thing is, I think I once had it to 4.3 but last year it suffered from the weird non-booting/non-charging issue (mine was solved from the battery pack adjustment fix) and then was running really slowly so I factory reset it. It reset to 4.2.2 JDQ39 and now won't install the 4.3 OTA update, same thing as what happened to everyone else. :/
I did not attempt to run the other diagnostic stuff that you posted in this thread previously as none of that seemed to work, the only thing that seemed to work is to re-flash, which would be fine, I don't have any data on it that I care about anyway. I have no experience with this so I was going to use the wug toolkit, but it seems that that website is down (?) I haven't found an alternate place to download that file yet. Can someone point me to an alternate download for wug's? I really want to fix this N7 now as I want to give it to a family member, TIA!
EDIT: Never mind, I found a download link at
http://www.softpedia.com/progDownload/Galaxy-Nexus-Root-Toolkit-Download-213077.html
I have a Mac, but with Parallels that runs Windows 7. I was able to get everything to work with a few hiccups - it froze during the first attempt similarly to nightfox7 above, the command line error said something about the bootloader failing (maybe this is the original problem with it being unable to do the OTA 4.3 update?). So I enabled force flash and tried again with soft bricked/bootloop checked and that worked, like it did for nightfox7. I decided to only flash to 4.3 and see if the N7 would then work on its own for the OTA update to 4.4.2, which it downloaded right away and is attempting to install right now............. YES! Looks like it worked, I have 4.4.2 KOT49H now.
Hoping this info may help someone else who stumbles into here with this problem, or help you smart people figure out what exactly this frustrating issue is with these N7s. Thanks for this thread guys!