As moritz says, WWW::Mechanize is great. In your case I'd recommend WWW::Selenium which I learned about here from dragonchild and have only experimented with so far. What I've seen is inspriring. Selenium allows you to record a browser session -- the tedious clicking about -- and replay it as a script with all the hook points and editability you'd expect. It also supports JS because you're actually running the browser with the Perl. You can certainly do what you want with Mech too but it would probably take so long to write the script that it would eat up the equivalent of 5 years of "every six months" of annoyance. Selenium might reduce that considerably.

You probably have an impedance mismatch, though. Scripting the data conversions/scraping is probably a significant effort and the kind of thing that is likely to have bad surprises. Getting direct access to the DB to write plain DBI would be likely to save you a lot of trouble (bad/missing data surprises, reprogramming something for 50 hours to save 5 hours of administrative browsing). Since you are in the company, I'd try to get permission to get at the data directly.