Refactoring db access and tweaking MySQL performance...need help

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http://www.linuxquestions.org – I'm working on refactoring a site I built when my PHP and database knowledge was caveman-primitive. While it has been running fabulously and profitably for years now, traffic is growing and it's starting to creak a bit under the growing load. I need to refactor a variety of things, but the database access is probably the most important. Yesterday, the DB server (an Amazon RDS instance) had its CPU maxed out and it looked pretty much like the CPU was maxed out pretty much all day long M-F during business hours. I tweaked some MySQL parameters to increase memory available for caching and it's (HowTos)