Try to avoid using any file manager (uninstall them all if it is difficult to avoid running them). So you will practice in using file manipulation commands.
Probably? They won't run with sudo normally (in xorg at least). And only those explicitly allowed to be run with pkexec by maintainers will do. Of course it is possible to evade this restriction, but you definitely should not.
I have no idea what you are talking about. The answer to your question is: this is impossible and this is done for purpose. Don't try to work in linux like in windows.
Use bash-completion, it is much faster than clicking menus.
every distro I’ve tried has a strong sense that if you’re using the GUI you don’t need or deserve admin controls
GUI tools are not suited to be run as root in general. Few ones that are have special measures taken to prevent gaining privileges by another process, e. g. run a background non-GUI process as root and GUI communicating with it as an ordinary user. Such tools (package managers, system tweakers etc.) are usually configured to get required privileges via polkit (e. g. pkexec synaptic to run GUI package manager in Debian). Don't use sudo to run GUI programs!
Everything seems ok. It is unlikely that the disk itself is dying. Maybe the problem is a bad cable or bus controller. Or something is wrong with the filesystem.
And also show
ls -l /etc/fonts/conf.d