That just further illustrates how flaky the whole upgrade process is. Apple really needs to tighten up on making it robust, performing consistency checks, and so forth.
I can say that one or more of the following seems to have put me back in business for syncing music, whereas before, I'd end up with one song per album, and most of the music wouldn't sync, OR, it would sync at a glacial pace after a certain number of songs had synced, somewhere between 3000 and 4000 based on the subsets of my master playlist I was syncing as an experiment. Even a "no changes" sync would take forever once it entered derp mode.
1. Reset sync history in iTunes.
2. A DFU restore of iOS 7.0.3 and setting up as a new iPod Touch.
3. Turned off "Convert to 128 Kbps", synced a subset of my master playlist that was failing before, unsynced those songs (erased them), and restored "Convert to 128 Kbps". This worked, but it was not a solution, because I need to transcode.
4. Created a new master playlist for syncing, which I guess I ended up doing after (3) because it was still derped when I re-enabled 128 Kbps. This is my best guess as to what fixed it; unfortunately, my scientific method had succumbed to frustration, and I don't have good records at this point.
I've now got 6663 songs on my 64GB Touch without any of the anomalies, which is a little more than half the music I had on it originally, and far more that I had been able to get on the Touch since first installing 7.0.3. Simply restoring iOS 7.0.3 and setting up as a new Touch without restoring a backup was NOT sufficient for 7.0.3, while it worked for the original 7 release. Once it started working, I was even able to restore a backup and get all my apps and settings back.