Do you see those 90% peaks live? Then just run top to find the culprit.
Do you see them after the fact, e.g. as a sar report? Perhaps process accounting will help
https://www.gnu.org/software/acct/ma...ccounting.html, or are there more modern utilities?
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It is my understanding that none of the apps running (apache,mysql,varnish) would show up as system usage
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If by "system usage" you mean system CPU, you are wrong. System CPU usage is accumulated when kernel code is executed. A process that issues many system calls, for example a lot of IO, would have a high system CPU usage.
By the way, consider updating to 6.7 (yum upgrade).