How did you end up with "a bunch of files"? You won't get the menu across, btw. You can only put _video_ files on the iPod, nothing fancy like subtitles and more than one language or bonus material (except as their own video files). But really: Use handbrake to create the MP4 file(s). It's not just a matter of transcoding to MPEG-4, the files also must fulfill certain requirements about resolution/bitrates etc. Handbrake is the way to go. Rip on that Mac mini and give her the resulting files so shen can put them on the iPod with that other computer which is iPod's home.
The "automatically synch..." feature of iTunes/iPod integration is not the most stupid, but the most _brilliant_ feature of it all. It keeps _all_ your iTunes and iPhoto media in perfect synch between your Mac and your iPod. It's just that some people don't _expect_ it to work that way and want to synch their iPod with various Macs and PCs, which is not the intended use with iPod.