I had a similar problem years ago, and I solved it by writing an injection routine into Devel::Examine::Subs.
Effectively, it uses PPI to inspect Perl files to find out all manner of information from them. The addition allowed me to inject code at certain points in the code for tracing flow.
This software can inject a routine to write usage statistics to a DB in every single Perl file you have. It will be consistent and reliable. With one command, you can inject as few or as many lines of code to all files across your platform.
I use it for new clients to baseline which files (and down to the subroutine) are actually used, and how often.
Feel free to contact me privately to discuss specific details, then if you go ahead, we can post the details here.