I've done previous points of your guide, but I don't exactly understand this one:
Does that mean that I have to install standard CyanogenMod 11 on my S3 and then replace it's system folder with the "Ubuntu" one I created?Use these following instructions:
Finally, get an otapackage cm11, then after the build, remove the system folder and copy over it the Ubuntu system folder.
It's necessary to fix META-INF folder also the wily or vivid tar.gz preinstalled script capable to install as an otapackage zip file.