Besides what other people have said, you can also monitor the resources your application uses directly (so you don't really need a perl monitor). Most significant slow-downs I've encountered involve the application waiting to use something (such as a database connection or physical memory (pagign)). Your basic sysadmin monitoring tools can help there.

Once you have some real time (or close to real time) monitoring of the resources, you can match up activity in the web server log with the data from the other sources.