Can't root Nexus 4 after 4.3 update - tried WugFre?s NRT and N-Cry Toolkit (with TWRP)

I have no problem with flashing. I already tried Wug's toolkit and it did not work, so I will try the ROM you linked...
 
Odexed is how the factory image comes. Some say the rom is slightly smoother and faster if you stay odexed. I never really notice the difference. Deodex allows for easier customization, like flashing mods and theming.

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Staying stock odexed will allow for future OTAs, while deodex will not. You would have to flash a similar updated rom as the one linked or a factory image and reroot


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In that case you can do what I did, dirty flash the above rom in the link. You can do this because you are essentially flashing the same build with only a security patch applied. Just skip the factory data rest. Flash the rom, wipe dalvik, flash SuperSU, and reboot. If TWRP offers to fix root, make sure you deny. This actually breaks root because it is wanting to apply an older method that was before the security changes. If this method helps you to maintain root, you would just need to flash the latest radio if you so desire.

Sent from my Nexus 4 using Tapatalk 4

So I finally got around to do exactly as you suggest above here (flash-wipe-flash-reboot with no TWRP "fix"), and while it fortunately didn't go wrong, neither did it go right - in the sense of obtaining root. Everything is just as it was except with the new version JWR66Y ROM instead of my previous "V" vers., but BusyBox or Titanium can still not access root.
 
All of that is was I did, minus the factory reset. I was told in the above quote that I could get by with a "dirty" flash (i.e., no reset) since I was not changing versions. Are you saying this is not true?
 
You do not need to factory reset. Although, considering you are flashing on top of an issue you already have, it is probably a good idea, but I realize you are trying to not lose data. Go back into recovery and, under advanced, try fix permissions.

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Does the SuperSU app allow you into it's settings? Try running cleanup for reinstallation from Google Play and then installing from the Playstore.

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Ah! Well, it turns out my SuperSU was "Disabled" somehow (from within Google Play somehow - it did not even show up on my apps screen!) and when checking settings I was going into an app called SuperUser (thinking I was in SuperSU) which wasn't helping at all! I deleted that, re-enabled SuperSU and now everything seems good - Titanium, BusyBox and other root-requiring apps ask for root and are granted, so I assume all is good.
Sheesh! Thank you for your patience and guidance! hopefully I am done now?

Will I need to do all this on every OTA update?
 
Ah! Well, it turns out my SuperSU was "Disabled" somehow (from within Google Play somehow - it did not even show up on my apps screen!) and when checking settings I was going into an app called SuperUser (thinking I was in SuperSU) which wasn't helping at all! I deleted that, re-enabled SuperSU and now everything seems good - Titanium, BusyBox and other root-requiring apps ask for root and are granted, so I assume all is good.
Sheesh! Thank you for your patience and guidance! hopefully I am done now?

Will I need to do all this on every OTA update?

Good to hear you are all good now. With future updates, depending on if it is a minor update or major update, you may just need to flash the update in recovery or you may need to wipe data before flashing rom and root app.

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