There aren't too many differences that affect your times and speed, but there are a few necessary changes to note.

Before anything else, the Japanese version can be downloaded here: http://kouri.kuchinawa.com/game_01.html (Requires setting your computer's locale to Japan, there are plenty of tutorials for doing that online)

Also, this won't list EVERY change made to the English version. It just lists those that can affect speedruns.

Obviously the Japanese version is in Japanese. The text scrolls faster in Japanese which saves probably a few seconds.

To get the ant painting in the Japanese version, you MUST to talk to the ant. This is not needed in the English patch for some reason.

To skip the story book on Japanese version 1.07 you need to replace the file "Map0028.lmu" in the Data folder with the one in the folder titled "「うごくえほん」が読み込めない方へ" (which sort of means "If the 'Story Book' fails to load"). In English you just have to choose not to read the book. (Should doing this be allowed? I think it should since it's an official patch.)

The part of the game where Gary puts in "Abyss of the Deep" to open the door is different on Japanese. In the Japanese version you actually have to type the name with the original kana. The painting's name is "Shinkai no Yo" (しんかいのよ) .

The door which Ib has to choose "Marvelous Night" is similar to the last one in which you have to type the name. This one uses both Hiragana and Katakana. The painting's name is "Midori no Yoru" (ミドリのよる) (Those first 3 characters are Katakana).

All of the other options and events are the same.

That's all I can find in terms of the "Promise of Reunion" and "Memories Crannies" endings. The "Welcome to the World of Guertena" ending might have a few important differences but I don't run that category so I wouldn't know. If I find anything else I will update this.