I have tried to extract the game data using Bandzip with Japanese settings and everything, so I'm kind of sure that the filenames are intact, but I also have a weird issue with installing the Japanese Run Time Packages for RPG Maker 2000/2003. The installer thing only works when using Locale Emulator, but the installation program crashes when it comes close to finishing. This issue may sound familliar to certain people, as it stops right at 44% and I think people have reported this issue before. Perhaps I should look into that more, and see if I could find a solution.
Of course, it could just be that I'm using Windows 10 and that I should wait until the game gets optimized for the new system.