Hey!! I've been using MySQL tuner through this process, but that mtop and munin are great resources!!
I was able to fix my own problem. In my MySQL my.cnf I added the line:
innodb_flush_log_at_trx_commit = 2
and wallah, suddenly my course uploads takes minutes instead of hours and my teaching staff are saying that the grades change instantly instead of minutes. I do get that if the server crash, 1-2 seconds before the crash anything inputted would lost but the risk, but in the scheme of things it's an acceptable risk for us.
I appreciate the time and resources you provided. I'm still going to use that mTop to help optimize further!
