Maybe an easy way to write a quick GUI for the app would be using the Tk module, which is pretty much platform-independant. It's fairly quick and easy to use, although it is a little limited in what it can do. If all you need is two file names and a "Go" button, it's probably ideal :)

There's a utility that lets you compile a Perl script as a .exe, called (cunningly) perl2exe, which is available here. It's not something I've used, but it looks like it'd do the job from the website.

Hope that helps a little ..
--Foxcub