Hi, I'm the author of the script and I just accidentally found this thread.
I'm glad that it helped (some of) you.
As some people have problems with themes and some forget to run it as root
I have modified the script to keep the themes on NAND and to check for the root user.

Upgrading the firmware OTA after using the script is supposed to work.
If you reflash you should run "rm -rf /home/var /home/usr" as root before using the script again.