Okay, that's really odd... could you make 2 ISO's, one before running the commands, and one after running them? Also, before you make the first ISO,...
Oh, I think I know part of the issue now. I forgot that running sudo actually discards any environment variable information (including $HOME), so try...
/etc/share/themes? Are you sure it's not /usr/share/themes? If it really is in /etc/share/themes, move it to /usr/share/themes (and update XFCE about...
For the record erm, I managed to put a fast and I think fully working server together by installing Ubuntu 12.04, then ZPanel, then memcache, APC and...