Nexus 6 E: Unable to mount Storage error in TWRP
This question is a little old and may be solved now, but the simple answer is: you don't have to do anything.  If your clean install of CM12.1 does not trigger this error, then that is the solution.  Do a clean install of CM.  Root is built into CM.  There is no compelling reason for you to be rooting your device, or even installing thing like SuperSu.   You can toggle root settings in Developer Options.