I think what Molly means is that perhaps it's easier to take a default or sort of standard audio track that is already synced to video (so the First Contact Blu-ray's audio) and sync the DTS Cinema rip to that. Sync it to that, and it'll naturally sync to the video as well. This is how I did it on Jurassic Park 3D and it worked pretty well and was easy.

As we know, the hard part with this DTS project is cutting and splicing the reels together. I continue to try and teach myself how to do this.