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.