Having recently done this on a fairly large codebase that grew organically (no design, no refactoring) over the course of four years, I feel your pain.
Writing a testsuite, on any level, is nearly essential for this. If you're rewriting an existing module, you'll need to ensure it's compatible with the old one, and the only sane way to do that is to test. If the old code is monolithic, it might be difficult to test individual units, but don't let that stop you from testing at a higher level.
B::Xref helped me make sense of the interactions in the old codebase. I didn't bother with any visualization tools or graph-creation, though. I just took the output of perl -MO=Xref filename for each file, removed some of the cruft with a text editor, ran it through mpage -4 to print, and spent a day with coffee and pencil, figuring out how things worked.
Pretty much the same tactic was used on the actual code. Print it out, annotate it away from the computer, and then sit down with the notes to implement the refactoring. If your codebase is huge (mine was about 4-5k lines in several .pl and .pm files, and was still manageable) you might not want to do this, though.