Here's what I know:
Both screenshots are the contents of y9.bin of the J and U versions of the game.
If you look the first column, it goes up by one every row, up to BA (which is 186 in hexadecimal, which in turn is the number of overlay files). So the rest of the row must be information about the corresponding file in the overlay folder.
To test it, what I did (and explained in my previous posts) is copy only the overlay_0000.bin from US to JAP, repack and start the game. This result in the rom crashing instantly.
Next I did the exact same thing, but opened the y9.bin in an hex editor and overwritten the first line so that it is the exact same one as the first line of y9.bin from the US rom, repack and start the game.
This only changed the menu text to english, but you could start any game, the rom does not crash anywhere (although the games are still 100% Japanese).
I pushed this further by replacing the overlay_0001.bin and modifying the y9.bin, but this time, the rom crashed when you start Megaman Zero 1 (Other games runs fine).
As for the data folder, I already explained but there is probably no need to change them, as they are almost identical in both version. Only the textures differs (meaning that both versions contains both japanese and english sounds).
I checked by swapping the DATA folder from US to JAP, and only the logos were changed, everything else was still from the JAP rom (blood, voice acting)
[Note: If you swap the DATA folder and start Megaman Zero 4, you get the english scrolling text + JP Ciel narration as intro].
