So you've watched top through the entire time autobackups were running?
"innodb_buffer_pool_size (>= 9.0G) if possible."
That means data size is near 9 Gig - maybe over. What's the size of a mysqldump of DB?
Bet what's using SWAP space is DB!
Some other items of MySQLTuner ..
Maximum reached memory usage:
Maximum possible memory usage:
Overall possible memory usage with other process is compatible with memory available
"Rather than 4x'ing my monthly cost"
Sounds like hosting with Azure as the Virtual hosting is expensive!
How many other Guest OS's are in/on same Azure box?
And how many courses are we talking about?