I would suggest not using Crypt::PasswdMD5, but instead using Authen::PAM, a module which allows you to avoid worrying about exactly how and where passwords are stored and makes customization in how passwords are authenticated easier. It may also avoid the need for your program to be setuid. The only disadvantage is that there are probably some systems without PAM, where this would not be an option, but in my experience most UNIX systems have it.

(update: no_slogan tells me that Slackware does not have PAM, for some reason.)