My initial response to this matter is that, all things considered, perhaps you should just examine all of the scripts and write a Word document that contains whatever comments you wish to make about them. Simply talk to “the equally befuddled persons who are doomed to come after you,” and help them along. I don’t necessarily interpret this requirement to mean that you should add POD-comments to each file. (But,
if at-all in doubt, ask your manager who gave you this assignment!!)
My opinion of Doxygen is that (a) it unquestionably delivers to you “what its designers intended,” but (b) that it is not terribly useful. It is, after all, merely a digital algorithm. I suspect that you have been tasked to “dive in to all of this (mess) and (please) come up with a useful set of bread-crumbs.” If Doxygen can provide you with a useful-to-you and-to-your successors part,</em. then by all means use it. But you, as a human being, will have to go from there to produce a final-product that is useful to the team.