I don't know how you guys do the extraction, but I'd like to share my own script, maybe you'll find it useful (and not just for Japanese).
1 - download this archive - https://www.dropbox.com/s/qs497t04e6760ad/translate.zip?dl=0
2 - open translate.lua
with your text editor and configure the encoding table for your own needs (you can write almost anything you want between "" for corresponding bytes)
3 - find text in the ROM
4 - copy bytes and past them into input.bin
with your hex editor
5 - launch translate.bat
6 - open output.txt
to see the result
Here is an example of how to use it - https://youtu.be/eIP3yUhFplU
Since bytes can contain some control bytes with different arguments (new line, pause, etc), which might happen to be the same values as text bytes, make sure to compare text with what you see in the game and check for minor errors.