I just finished a new tool which can replace all files in the rootR. I also attach a modified unpacker script that dumps all files still compressed and a modded tocdump (dumpextsize) that only makes a filelist, but this time it saves the uncompressed size of the files. You will only need this list.
To repack, place all the files (uncompressed or not, doesn't matter) to a directory. For best results, unpack both US and JP keeping compression then copy the files from the US dir over the JP dir. This means you can also use big files like voices. Running the repacker it will take some time since has to check 2111 files, but it will finish.
I can't test the results right now but the new file should work correctly with the unpack script.
Note that this only works with the (JP) rootR.cpk, with exactly 2111 files.
About the trophies, it could work, there are some differences in the data part, but most of the file is same in both versions. Or we can just replace the text in it, it looks like they are in same order.
there are minor visual gliches, like the numbers are too close to each other in the menu, there is a black bar when you enter a new place (missing texture?), and some letters may not show if the skit line is too long, but nothing serious with the gameplay.
i don't remember problems with monster names, but I will check it.