In someways you should first consider how much code you need to examine and your timeframe. Do you spend 5 days goofing with the computer when if you simply printed and read the code, taking notes, would provide the overview you need. And it only took 2 days.

Look at cpan with keywords like, profile, debug, dbug, trace, etc. *grep'ing is problematic in that method calls are on objects, but you need to know what the object is to be able to know which method is meant.

Moose provides meta info on classes etc. Code needs to be written using it...

Debug::Trace has a unique approach.

There have been various attempts at providing a filter for Doxygen.