Not sure 'give up control' is accurate description. OP is in K12 world ... which is not like what you know Mr. V! OP is in a state of US that has an entity that provides services/servers for schools - they do have engineers on staff but seldom do they get involved with a school unless called upon. OP has a WHM/cPanel setup ... the caddie of such hosting. OP was pitched 'automatic updating of moodle' by Installertron folks. He decided to try it. It failed. Am guessing site restored and that's when things got slow.
Engineer called in to fix ... that person isn't that well versed in Moodle's. And we know, that Moodle is senstive about many things ... little things that add up.
Ok, now that you have the story ... some details ... WHM/cPanel setup had Easy Apache - a misnomer really as that deals with PHP versions + PHP extensions + PHP settings of the PHP chosen for a service. PHP version to run version of Moodle was ok but settings were not ... max_allowed_packets - not set high enough. The other item which is why the meeting with Engineer ... config of MariaDB. A moodle set to use localhost should be using sockets not TCP/IP stack for communications between apps and DB's. And sockets don't really need the encryption (TLS certs) during communications. Those 2 would slow a moodle down. A mysqltuner install and run showed Innodb buffer pools and data size settings needed be tweaked upwards a little. Had to run tuner with DB user in config.php of site which was not root user. Thus the report not as good as it should be ... again, another reason to bring in the Engineer.
While in that server via WHM Terminal - ie, root - did setup the site with the only 'easy button' known to work ... that of git versioning and with a couple of shell scripts ... one to backup the site (OP confessed wasn't doing that often) ... and one to update Moodle version when OP is ready ... easily ... with the 'easy button' of git.
So there ya have it! 
'SoS', Ken
