The sounds in the cutscenes have a layered sturcture. There's one audio file for the ambient sound effects that are out of sync, another one for the speech and a third one for music.
I took all the audio files of the ambient sounds layer of cutscenes, and CHANGED their sample rate from 22050 to 22380.
You may do it yourself too, or you can download my fix. The key is to CHANGE the sampling rare, NOT CONVERT.
This means that they are played back 1.5 % faster. This way even the long cutscene of Kabuto's first appearance stays in sync till the end.
Here's a 7z. Replace the Stream folder with this one and have an excuse to play this amusing game once more

http://preview.tinyurl.com/y7qzqjq7