Well, first of all, if you are running out of battery, first flash the custom recovery.
fastboot flash recovery recovery.img
I would recommend Philz touch. After this, reboot your phone and enter in recovery presing power + up. Here your phone will charge.
If it doesn't work, try with another fastboot. That could be the issue, too. After you have enough battery, try again to flash RSD Lite to Stock. If it works, then try to flash the partitions. If nothing works, please let me know, let's find a solution
I'm not sure if that would be an issue...