the error is raised because some of the packages listed aren't yet in the ubuntu repository.
You can try to install specific packages with the command 'apt-get install [package1] [package2] ...
The packages that are lsited in the previous link from the ubuntu's package pages are a safe bet to install.
About your second question we have a module to control a webserver but isn't ported to Ubuntu yet (eBox originally runned on debian ).
WE haven't a module to control mysql.
I am not sure what you mean with a file manager module, if you mean a module to be able to share files in a network, we have the ebox-samba module that provides this feature.
Cheers,
Javier