You are obviously well set up and ready to go.

Then my next step--after running everything through PerlTidy to get a consistant layout, and making sure it doesn't break anything--would run it all through perlcritic.

Or rather, I'd run one or two of the larger pieces of code through, and then manually cross-reference the output with the code, and decide which of its protestations are bogus, and work out how to turn them off. Once you've turned it down to the point where it is only bellyaching about things that you agree are worthy of note, then it would be a fairly painless process to then pass the entire codebase through.

That would give you two things:

1. An indication of where to start concentrating your refactoring efforts.
2. A set of documented (PBP) reasons that you can take to management as justification for the refactoring efforts.

Maybe that suggestion will go some way for my grandmother-eggs-vacuum thing. It's often difficult to access where someone is at from the wording of their questions.