If you have a webserver and find you have high IO/lagginess MySQL is one of the first things to check. It turns out MySQL was my problem and it was creating a high load on my server, especially for IO.
How to Enable MySQL Slow Query Logging To Find Slow Performance/Queries
Add this anywhere under [mysqld]
log-slow-queries = /var/log/mysql/mysqlslowqueries.log
long_query_time = 1........