I haven't looked at it to be honest. According to HomuHomu the easiest solution (exchanging the text files) crashes the game if you try playing it further than the introduction sequence.
I can test some stuff later on and see what works out, it might require some extra files that are located in the other folders. After diffing the trees all I could really find was a "logo" file named "logo_exs.bctex" hidden in the menu_field folder in the American one that isn't in the Japanese one and it might be crashing because that one is missing. It's just that one, the different voice files, some extra staffrolls and the files in /text and /textAndData that are really missing from the Japanese one. Some of the textures have different md5s from the Japanese release which I assume are textures that have written text on them, but I hardly think those could have an impact on it not crashing.
Other than that, the English one is really trimmed down with a lot of "MAP" files and some testing files are removed. I presume those are debugging maps or some maps that got cut from the English release?
Diff the JP and EN trees and you can see the differences. If adding the missing files from the English release to the Japanese one doesn't solve the issue, it's pretty hard to guess what files makes it crash, so if that happens I'm out of ideas.
Edit: Well, I've replaced the necessary files, but I have no idea how to repack the ROM and apparently my Google-FU is not good enough to find any relevant super-secret repacking tools, so I guess that's as far as I can go.