Debug script using Php_Debug 1.0.3 on a shared server

I have a website on a shared server. i see major spikes in the cpu resource usage graph in cPanel. the spikes don't follow a pattern and are different in magnitude. my website has around 300 pages, with around 10 thousand files to download (mp3 and pdf). it has a php script counter for page visits, and another counter for number of downloads. It is a custom php website, not a CMS system. I have "Php_Debug 1.0.3" module installed on my system, and can install Pear and PErl modules but NOT Pecl. I need someone to perform debugging tasks to see what is causing these spikes to happen. I attached a screenshot to demonstrate the spikes.