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Oh wow - this is incredibly helpful! I have been working on some shell scripts to do this over the last week and just replaced the majority of the script with GNU stow and it is much more elegant in its simplicity. Kind of surprised I have not heard of this tool.
Using https://github.com/Czahrien/shell-config-files if you are curious.
I settled on having a main dotfiles folder containing packages that will always be stowed, a platform folder with a name derived from uname -s -m and a host folder derived from the hostname.
It's possible that those three lines being logged rapidly is the major cause of the lag you've been seeing.
The cause of those ACPI messages could have to do with your motherboard manufacturer doing something "non standard".
https://forum.garudalinux.org/t/dr460nized-is-frequently-freezing-and-30k-lines-of-acpi-errors-per-second-when-i-look-into-journalctl/16057
Provides some instructions for masking the L09 GPE that you can try. I'd also follow their recommendations to do a memtest etc.
If the lagginess goes away after following the instructions then chances are the log messages were the cause of the lag. As for why the issue began in the first place? It's harder to say. It could be that a recent kernel update introduced some behavior which triggered the issue - so perhaps downgrading the kernel to a version from a few months ago is worth a try.