I've aligned the ~20GiB WOWOW 1080i capture to the R1 DVD (I prefer its 5.1 AC-3 audio to what's on the BD).
This took some work because two frames were dropped which caused a cadence break and prevented "Force Film" from working in DGIndex, so I had to manually IVTC it even though the stream used soft pulldown (ugh!).
After padding the beginning and end with appropriate amounts of black frames, I used my shot-change-detection+diff method to verify that the two are synchronized. They are. I then used IsCombedTIVTC() to verify that no combed frames were leftover from my manual IVTC. None were.
So... yay!
I now face the challenge of removing the few instances of burned-in JP subtitles. Does anyone have a list of which shots have them? If not, then I'll watch it once through and take notes. Thanks!