Another few suggestions that may be of some use.

• Port everything over to a test box so that you can make changes without worrying about the effects on other scripts as each one goes "live"
• Write a script that will go through each script on the text box and add the 2 lines "use strict;" and "use warnings;" because as we all know, that makes for cleaner (and more portable code).
• The next thing I would suggest is to see what you can port into modules. You said that there were a lot of subroutines that were just copied and pasted with slight mods. If there can be turned into reusable code, that would take care of a lot of code cleanup.
• Harping on reusable code, see what's out there (in CPAN) that may already perform the functions that the scripts do (and it may work more efficiently). You may have to rewrite a few scripts to work with the CPAN modules, but all in all, it sounds like that's the least of your troubles.

Good luck

Eric