Alright, Generally when I install custom roms I like to do it manually in recovery. That way I know the correct things get wiped.
So my first suggestion would be to first get into CWM manually. You can do this by first going into fastboot mode by holding vol up + vol down + power while the device is off. You should see an android laying down with it's stomach opened up and the word start in green at the top. Use the volume down to change it from start to reboot recovery, then use the power key to select. After that, the device will boot into CWM.
Once in CWM, you are going to want to preform a couple of wipes to make sure anything from the stock rom is gone. You will first select factory reset from the main menu. Second will be a wipe cache from the main menu. Third will be format system in the mounts and storage. Fourth will be format/wipe (can't remember which) dalvik cache under the advanced menu option.
Once all 4 wipes have occurred, go back to the main menu and go to install from sd card, then the option to let you pick. Locate where your CM10.1 rom and gapps are and flash those in those exact order 1 right after the other. Once done, return to the main menu and reboot the device. It should boot up now, though it may take a couple of minutes, but no more than 5.