All went well with the root process.
Let the phone reboot like it needed
Used the APK from chainfires zip to install supersu on the phone.
When I installed that I allowed it to update su and then disabled knox.
rebooted the phone and verified all was able to power up again okay.
Since doing that I notice that the phone is staying pretty warm without any use and screen off and is being held awake by the kernel. (according to gsam battery monitor)
Has anyone else noticed wake-lock or battery drain issues after rooting the phone with this method?