2016 (January)
Nethunter 3 installed on Nexus 7 2013 (WiFi) prime ROM factory Android 6 (Marshmallow)
via basic nethunter guideline.
 
2015
 
Nexus 7 2013 (Wifi) - Nethunter install on 2nd ROM (Multi-ROM boot).
Before starting check if a newer Nethunter version is compatible with a higher Android stock version. 
Many of below steps can be skipped if installing Nethunter on Single prime ROM (use the Nethunter guide). 
Beware, not all ROMs are compatible, some work very slow. 
The used stock ROM image-razor-ktu84p (prime) and pa_flo-4.6-BETA6-20141103 (second)
with Nethunter flash-zipped over perform pretty well.  
A) Restore Android 4.4.4 (back from stock 5.0.2) to ensure Nethunter compatible core
   may not be needed if a new Nethunter version is released 
   (then install / upgrade via zip-flash)
1) On PC: ensure SDK hardware (USB) drivers are installed and path defined
    (Nothing to do if Android project / SDK is correctly installed, ...\SDK\platform-tools)
    Download unzip &: image-razor-ktu84p.zip 
3) Connect Nexus device to PC and from unzipped directory run flash-all.bat
    (remove -w in conf to preserve SD data) 
     => back to 4.4.4 
B) Root (again needed if above step 3 was done = back to factory settings) 
   Install Multi Rom (TWRP), install 2nd ROM (can't be stock) and 
   flash-zip Nethunter over 2nd ROM. 
   
1) Set debugging mode ON in developer section
    (if developer not visible click 7 times on build number)
2) Probably best tool to facilitate root is http://www.wugfresh.com/
   Nexus root toolkit, Download, install  (needs same USB drivers as A1) 
3) Launch Nexus root kit, ensure device is auto detected 
   if not detected in order of problem frequency (A1), (B1), the root kit outlines more options.
4) Perform 
     a) unlock (usually not needed if A3 not done) 
     b) root  
B) Add 2nd ROM
1) From Google Plays, install Multirom manager on prime stock 4.4.4 rom
2) Download 2nd ROM to Nexus, (can't be stock). (was installed with pa_flo-4.6-BETA6-20141103) 
3) Boot into Multirom TWRP (stop device, then press start and volume-up button simultaneous.
4) Select a) advanced b) Multi-ROM c) add ROM
5) Select a) Android b) Zip c) select ..ROM.zip d) process install
6) step TWRP menus and reboot device but ensure to cancel automatic reboot in
    prime ROM - instead select 2nd ROM.
7) Process basic set-up of 2nd ROM (wifi code etc) - mandatory before C)
C) Flash-Zip Nethunter
1) Download Nethunter Nexus 7 (2013) -
    to Nexus 7 (Virtual SD directory, last used version 1.1).
2) Boot into Multi-rom TWRP 
    (stop device, then press start and volume-up button simultaneous).
3) Select a) advanced b) Multi-ROM c) select list ROMs,
    d) select 2nd ROM to flash-zip Nethunter (pa_flo..)
4) Select a) flash Zip b) Nethunter.zip c) wipe to perform flash-zip
    (ensure battery loaded or connect charger).
D) Boot into 2nd ROM and finalize Nethunter module installs 
    Ensure battery fully loaded or connect charger.
   (e.g. follow prompt for metasploit install, account PW for community version)
   Initial boot and set-up takes time to get additional downloads, cache and DBs set-up.