Drupal 6 - How to check which module is caused high loading(high CPU usage)
I'd also try a PHP profiler which gives you a lot of metrics. Take a look at the XHProf module. Here is an excerpt about it from the module's project page:

... allows you to profile your Drupal application using the XHProf profiler from facebook.
It also provides a native Drupal UI (as opposed to facebook's original php front end) to view the profiling data. Having this in Drupal provides several advantages:

Simpler setup
No need to setup extra vhosts
Limit access via roles and permissions
Use alternative storage backends such as MongoDb