Albert, I just read this thread almost from the beginning, as we were in Germany memorating WWII.
Now you have ensured that the waviness is not coming from the disc, I have a completely different suggestion: LISTEN to the separated sync signal and LISTEN to the signal coming from the sync pick-up of the disc. You can do so using a cristal in-ear receiver, or with some form of LF amplifier and a loudspeaker or head phone.
You should hear a humming sound, the same that you hear from a black video signal (NBTV CD No 1 track 2, 3, 4). Listen to the video channel (Left) and get used to the sound.
Now listen to the separated sync in the same way. Assuming that you use the circuit from page 13 of the new bue Handbook, listen at the signal "sync out" of the LED-driver circuit. You should hear the same sound, which should be absolutely independant from the video content on all tracks of the CD. Be sure that you will hear all irregularities in the humming sound. If you have some potentiometer to adjust the sync level, try that and get the best humming sound you can get.
Then listen at the sync as picked up off the disc. That should be at pin 3 of the 4046. That should give you a comparable sound, however that is not really true. Unhappily you don't have access to the real signal as this is only available inside the 4046.
I hope this will help you.