At least you have modules. You should be able to organize those modules into logical groupings. Once you do that, focus on one grouping at a time, writing lots and lots and LOTS of tests. Test everything, anything ... if it moves, test it. Heck, test it even if it doesn't move. (You want to make sure it doesn't start moving!)
in reply to Re^2: Analyzing large Perl code base.
in thread Analyzing large Perl code base.
Note: you will find that many of your tests will be wrong ... and that's good. :-)
Update: As adrianh says, you shouldn't write whitebox tests - you should be writing tests for how the rest of the code expects your modules to work. In other words, API tests. Remember - you're planning on ripping the guts out ASAP. You just want to make sure that the rest of the code doesn't die while you're working.