I then proceeded to update SuperSU using the following link: http://download.chainfire.eu/supersu which was the update v1.99r3.
Using TWRP I flashed this and root is working for most apps i have tested: titanium, adblock, root explorer. So root is back.
However whenever I load up SuperSU I keep getting the following message: "The SU binary needs to be updated. Continue?"
So of course I have done this and let it use TWRP to flash. Let the phone boot up and upgrade the app as it needed. However on next load up of the app it asks to do the same yet again.
I feel as though I'm forgetting something as it's been a while since I've done this. ( use to live on flashing when i had my SII)
My Nexus is Stock ROM. CF-Auto Rooted. TWRP Recovery. Nothing else is modified.
Help would be appreciated, even though I don't go into supersu all that often anyways.