I'm not an iPod expert (never had one), but I would go about it a slightly different way. I like the way my system works (It works great with XBMC, the Empeg, the Karma, and iTunes over the network), hopefully you can get some ideas.
I do store all my music on a Linux fileserver. A long time ago when I started ripping my music, I kept all the filenames and directories accurate to a format (%A - %AL/%N %A - %T where %A = artist, %AL = album, %N = tracknumber, %T = trackname). With a slightly dirty but reliable Perl script, I re-tagged everything in one big swoop. Then year, genre and albumart was added on an album by album basis. That sorted it out nicely.
About 40% of my music was in FLAC (I don't know how to tag these btw). Another little Perl script later and I have /data/raid/lossless/ which is the original archive, and /data/raid/lossy/ where everything that was MP3 already is just symlinked over, and all the albums in FLAC are transcoded to.
/data/raid/lossy/ is the music directory for
mt-daapd, which makes all my music magically appear in iTunes on any machine on my network.
I would plug the iPod into the Linux machine and use something like
gtkpod to put music on it. If you don't have a monitor attached, or X configured or whatever, you can always run it in a remote X session. It is easy to do on a Mac, or another Linux machine. Windows? I have no idea.