So, a radical edit, since I'm still having issues, and it's NOT the upgrade process, it's just the sync process.
Anyways, when I sync my phone to iTunes, a lot of my song files disappear from my phone. The songs appear to be on the phone, the playlist has items, even album artwork. It seems all the metadata is still there. Just the actual songs are missing. Trying to play most anything just fails with a missing song icon on the device as it quickly skips most files in the playlist. Files from iTunes itself do have the files deleted from the device, but then these are streamable files, so I actually get to play something as they stream from iTunes. The iTunes bought files still show up as not on the device though.
Another, probably related, oddity is the total unreliability of the free space indicator in iTunes. I can delete playlists from the sync, and free space goes down. I have the same rough group of playlists selected for sync, and free space varies by as much as +/- 4Gb.
So, most playlists lose all songs from device, and only streamable songs (read: bought from iTunes) get played. Individual Manually Added Songs are lost as well. To fix this, besides the turning on and off of music sync, on and off of playlists to sync, I tried a device restore, and it helped on the one sync, now the files are gone again. The upgrade to 8.0.2 didn't do much (thought helped battery life a bit).
5s + 8.0.2, Mavericks + iTunes 11.4