Booshman said:

Would it be possible to use the LD for colour reference with avisynth?

Yes.

I think the japanese subs are hard coded and sometimes they cover the movie image. Luckily there are no subs that extend out of the black border during the 2 extra scenes.

Until subtitles are confined to black borders (and it should be the case, as AR is 2.35:1) there will be no problem... could you please post some examples of subs out of black borders?

Wouldn't it be better to match bluray to the DVD?

Maybe... following the thread, it seems that laserdisc has a better color grading, but I'm not the expert here...