Debugging this code is a whole different game, and I'd really appreciate some input from other monks who've dealt with this type of problem.

I'd recommend reading Perl Medic and Working Effectively with Legacy Code (the latter isn't Perl specific - but is chock full of useful advice).

I would not spend any time fixing the code if it's not breaking (assuming you're not being paid to review/fix the code). However evil it may be - if it's doing it's job leave it alone.

Instead - every time you need to fix a bug or add some new functionality just test/refactor the bits of the evil code that are touched by the changes. I've found incrementally adding tests and refactoring to be much more effective than any sort of "big bang" fixing things for the sake of them approach :-)

If you are being paid to do a review/fix then Perl::Critic might give you some useful places to look.