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As PornDiscounts said, indexes are likely to help, but really you need to profile the code.
AnimeFevers, that's what you're looking for - somebody who knows how to profile PHP and how to profile SQL queries. That's absolutely the first thing you do in a case like this, not guess. You spend a few minutes with the profiler to know EXACTLY what's using all of the CPU.
AnimeFevers, I've been teaching this stuff for twenty years. My work includes contributions to the Linux kernel and the Apache http server, so you're already running my stack. If these other guys don't get you taken care of, hit me up. Or if adultwebdev does the profiling but then wants a second set of eyes on how best to fix it, they can hit me up. I'm not cheap per hour, but it might be worth a 15 minute call after you have the profiler results.
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