by Ken Task.
"Moodle instance is absolutely massive"
Maybe should have started with a description of the system ... all in one server? or is DB on dedicated and is moodledata on dedicated?
If you haven't check on the health of the DB server/db's and DB server is either MySQL or MariaDB, suggest installing MySQLTuner - a cli perl script.
Run with superuser creds for the DB server. Recommendations at bottom of the report might indicate some tweaks are needed for DB server. At the top of that - tables that are in need of optimizing with the command to do so.
'SoS', Ken