UPDATE:

I've finished downloading the DVD9, so I'm entering the final phase of this project - doing it!

Anyway, as of now, all audio tracks are finished.

Main Audio
Slowed down 4%; pitch has likewise been lowered 4%

Commentary 1
Slowed down 4%; pitch of original has been preserved

Commentary 2
Slowed down 4%; pitch of original has been preserved

Isolated Score
Slowed down 4%; pitch has likewise been lowered 4%

This means that for the commentaries, the parts where they are speaking preserves the correct pitch of the speakers' voices, while the portions with movie audio (when they are not speaking) retains the 4% increase in pitch caused by the PAL speedup.

The main audio and isolated score have been slowed down and the pitch has been lowered to compensate for the speedup and pitch increase caused by the PAL conversion.

You can tell by listening to the beginning, as for the first 5 seconds or so, each track has the exact same audio. Tracks 1 and 4 definitely sound lower in pitch than 2 and 3 (it's only music at this point), but all 4 tracks conform to the new 89 minute length (the PAL version is 85 minutes).

Now I just need to work on the video. I have both a full-resolution 720x576, 25fps PAL file, and a 720x480, 25fps "hybrid" PAL/NTSC file.

So, here's my question - I can CinemaTools both of these to play at 23.976fps. Should I do it to the full-res PAL version, fix as many interlacing issues as I can, then down-res to 720x480, or work with the already-down-res'd file from the start?