What I don't get is why you didn't see the relatively low cpu usage on the database server and the super high ones on the webserver immediately in a nagios (or similar) dashboard.
It's because they don't have a simple rollup dashboard that you can see that at a glance, like most places. Can you imagine if your car just showed you an event log for a door open, oil, turn singles on etc. that's what most monitoring systems are like these days.