As someone who's taken over a similar project in the past, I'm going to give you a piece of advice you're not going to want to hear. Do it by hand. Do not use a tool to do your work.

• Tools don't understand architecture
• Tools cannot give you proper naming
• Tools cannot tell you how to optimize code
• Tools cannot give you new features by noticing commonalities between dissimilar areas
• Tools cannot comment confusing code
• Tools cannot create the third and fourth levels of modules/objects - the basic infrastructure that the code users run depends on, but that users never see

As if that isn't enough, you're probably going to also need a whole bunch of documentation. I'll bet you don't have most of the following:

• Project description
• Architecture document
• Test plan / Test suite
• Use cases (or other user-design tools)
• Design documents (both high- and low-level)

Those documents are at least as important than the code, because they tell you what the code is supposed to do. The code just tells you what it currently does. Are you sure that what it does right now is correct? How much are you willing to bet?

Furthermore, most tools aren't able to use many of the reasons to use Perl in the first place. For example, I doubt a tool could reasonably handle

• Array operations
• Hashes in their non-trivial uses, especially as a way of passing named parameters
• References (especially scalar, glob, and sub references)
• Multiple return values from a subroutine
• Context-aware subroutines
• Complex data structures, especially dispatch tables and the like
• Objects, in all their glory
• The use of die, eval, and sub
• Correct scoping of variables

I hope you really choose to do this by hand. It will take about 3-6 man-months to do it. (I'm not kidding - it won't take that long.)