None of the symptoms sound the least bit like an MBR error. Typical victim of 'Dr.House' (diagnosis base on little or no evidence).
The idea of running smartctl diagnostics is not warranted at this time - but it's simple, cheap and eliminates a possible HW cause.
Same with memtest
If the system runs slowly then the place to start is by examining what is running and eating up performance.
I don't buy the OPs story that a mysterious bevy of apps run all on their own due to malware. More likely he doesn't understand all the kernel threads and services and cron jobs.
When the system is slow, run
and indicate the results. Post the entire output of free ,and an yprocesses using mych CPU in 'htop'. Is your system swapping ? and/or What process is hogging the CPU ? are the two critical questions.
Until we know that there isn't enough info to diagnose.
---------- Post added at 10:39 AM ---------- Previous post was at 10:13 AM ----------
The MBR has no files and the only 'attributes' are things like wither a partition is bootable or the partition type.
The fact that your first install of Fedora took forever to update might have been diagnosed at the time - but not after a reinstall - so that's nearly pointless history.
The speed of a fedora yum update is NOT enhanced by an encrypted filesystem.
80G vs 96BG is a real and testable issue.
As root this command will show the hardware addressible sectors according to the disk controller
hdparm -I /dev/sda| grep "LBA "
and this will show what is in the written disk geometry ...
fdisk -l /dev/sda | grep total
I get numbers like ....
LBA user addressable sectors: 234441648
255 heads, 63 sectors/track, 14593 cylinders, total 234441648 sectors
which should match.