I killed half a day trying to figure out what's wrong with my HDD, and trying to restore parts of the system from a backup, but then found out that the problem was in another place.
So if you run into the same issue the cure is simple.
sudo rm -rf /private/var/log/asl/*
Apparently there is some problem with the log files that cause circular read/write calls, so when you nuke the old logs, it will get just fine
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