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Before I ask, I have very limited knowledge of ADB and have been using "interface" like programs for all my Android root/flashing/pushing.

I bought a stock Nexus 6 and knew I wanted a custom ROM. I settled on Cyanogenmod. Somewhere during the process I messed up and had to start over. I must have unchecked/checked a box I should have because I kept getting the E: Unable to mount Storage and cannot see my phone in Windows Explorer as an MTP device. So I did a complete factory reset, flashed the stock ROM and it seemed to resolve the error. I then flashed CM 12.1 again and started the daunting process of reconfiguring my phone. I chose not to restore my backup because I wasn't sure if the error would come back too (n00bie, I know). Then I also made the mistake of allowing the OTA CM update. Well I lost root as a result. So I attempted to root again but it got stuck at the boot logo. In a panic I booted into TWRP and dirty flashed CM 12.1 using ADB sideload. All was good, I re-rooted again successfully, but now I am getting the same E: Unable to mount Storage error again.

So I guess my question is, how do I do a backup so I do not have to reconfigure everything again and still be able to flash the stock ROM. Or do I even need to flash the stock ROM again, can I do a factory reset and flash CM 12.1 or will my error not be resolved?

Thanks in advance.

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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.

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