So to make it work you're gonna need to remove all the files associated with root and scripts that interfere with the kernel (Ie they both try and so the same thing)
So in the Krypton folder in the zip delete recovery, root, superSU
Then go through the updater script and anything to do with those folders and the files in them needs to be deleted. Just use your instinct. If you deleted it then don't let the updater script try and flash it or it'll throw an error
This way you remove all conflicts and it can boot after flashing.
Flash kernel directly after flashing ROM so you keep recovery.