Alright, at this point because of the error, there's 3 options that we can do. 2 are a little more difficult but will save your data. The third one is to flash the whole factory image through wugs and thus lose your data.
The first option is move the zip file to a computer, edit the script file to remove those assert checks, move it back + rezip and flash that result.
The second option is to partially flash the factory image through bootloader manually. Basically we would manually update the bootloader & radios & kernel, flash the system through fastboot, then boot into cwm and clear out the dalvik cache. Then after first boot we would re-root.
The third option is a full factory image flash through wugs. This would be the easiest and potentially quickest, but will result in loss of data.
The choice is yours.