This is a problem in ALL linuxes as far as I know. When Linux gets IO-bound, literally everything gets stuck and it's insane. My mouse cursor position doesn't depend on my hard disk. I have a dozen cores. I don't understand. I thought this kind of issue was solvable on a single core with just a round robin scheduler. How come things still get stuck?
It could be that the problem was that I installed every DE I could find to test them, but even after uninstalling a lot of things, the system never recovered its original speed.
I installed Linux Mint on the same hard disk and things run smoothly. In particular, I love how Cinnamon actually keeps the list of applications in memory instead of starting a search every type I open the start menu. The DE has its shortcomings but it's pretty decent otherwise so for now I'm happy with it.
P.S.: also when I tried to use git with apache, checking out overwrote my SELinux types and contexts, which meant I had to figure out AGAIN how do configure all this stuff just so I could access a wordpress site in localhost that was saved in my home folder. For a while I just gave up using branches in git. Now I just use Mint.
For GUI notifications open the sealert app and disable alerts. For journal/syslog reports disable the setroubleshoot daemon dispatch plugin for auditd:
sed -i 's/active.=.yes/active = no/' /etc/audit/plugins.d/sedispatch.conf
service auditd restart
You can also uninstall the setroublshoot-server package completely, and all AVC denials will continue be reported separately outside of the journal.