I'm actually working solo on this. bavaleone kindly shared his audio file with me though. I'm syncing to the 98 DVD audio plus The Fort scene (both shown as a green band in the screenshots above) so my final product will be quite different.

I will upsample my LD PCM audio to 48kHz and then proceed with synchronization. For the fort scene, I have decided against using the DD2.0 track. Instead I have made a custom mono 2.0 WAV file using the 3 front channels (L,C,R) of the DTS audio. It needs to be attenuated a bit now since it's louder than the LD PCM.

In the 2nd screenshot above, you can see stretching at the bottom of the Mondo BD frame of Tuco reaching for his pistol (right side). You don't have that issue in the frame to the left (MGM DVD). Yet the number of frames is identical between the 2 sources for that particular segment of Tuco tumbling and crawling to his gun. Hope that clarifies things.