Your situation made me think back to my early days, facing the same sort of problem with masses of C code; back then (before internet connectivity was common), I actually wrote my own code indexer in C to read a bunch of C source files and print a simple table that lists the functions defined in each file, and the subroutines called from within each function. It really helped.

So, how hard could it be to do that in Perl? Well, not that hard, if you're willing to be content with less than (but usually close to) 100% accuracy in the "precision and recall" measures of subroutine detection.

It's a real bare-bones, quick-and-dirty, not-too-subtle attempt, but it's here in case you want to try it out.