Through testing of our server, I have come to the conclusion that our server is somehow limiting usage per user to MySQL.
When I run mysqltuner.pl, the script pegs one of the processors for several minutes at a time. While this script is running (from Account X), Account X slows to a crawl. Requests to X's web assets are extremely slow. However, requests to other accounts' web assets (i.e. Accounts Y and Z) run quickly and mostly without delay.
Is it possible that there are some limiting mechanisms in place that are enforced via MySQL, CPanel, or some third-party tool?