Nexus 7 2013
Tried first to install 'over the top' of Nethunter 2.0. All appeared to be ok, but on a reboot started moaning about a few files not found (old version) & then threw up a lovely unstable OS warning. So a complete wipe sorted that out.:-)

Have had similar issues to others about access denied, files not found etc. Even apt-get not recognised. Halfway through installing kali-linux-Nethunter I noticed it flashed up about being granted SU rights & then that's when it all went to pot.
On investigation into the SuperSU app, the log is full of entries about Kali app making requests for features only provided by SuperSU Pro. So maybe that's the issue?

Cheers,