I have found several utilities to be helpful for just this sort of thing.
When I asked something similar in the FullPage Chat, castaway pointed me in the direction of podgen, which will jump-start the process of commenting your monolith.
DoxyFilt* is a filter than allows the source-to-documentation tool Doxygen to understand Perl. Once you have your source commented, documentation becomes absurdly easy.
Perl::Tidy helps clean up your source and make it more readable. Perl Builder and ActiveState's Komodo may also have some helpful options or utilities.
Update: Seeking advice about learning another's code and Reverse Engineering Perl Tool? also contain excellent suggestions.
* Update: 2005-12-28 Kudos to both john_oshea and tfrayner for alerting me to the fact that my link above has been rendered usless by the foul creatures known as spammers... I have found what appears to be a good link to obtain DoxyFilt; the most recent version seems to be from August 24, 2005: Doxygen-0.84.tar.gz. Thanks again, guys!
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