For what it's worth, I might as well post how I ended up solving the problem. Turns out, there were only two files that had filenames too long for whatever reason for iTunes to deal with. I ended up discovering those files because tar choked on them as well. I "deleted" those two particular songs from my PC's iTunes and asked the PC to consolidate the tracks. That worked fine, saving me from the hassle of writing my own sync software. Then, I just moved those two long-named files over by hand, renaming them to something short, and having the PC iTunes add them into its database. So long as you don't have iTunes "managing" those wacky files, they can have whatever name you want.

Ultimately, if iTunes was only smart enough to recognize the "long filename" error and deal with it, then everything would have worked the way I originally intended, and I never would have had to learn how bizzare the world of Unicode can be.