I just prepatched the game myself using
HackingToolKit. You need to unpack both the English patch CIA and the game itself and just copy the files over.
*save a backup copy of the original game in case something goes wrong
1. Acquire the English patch CIA from this thread and the original Japanese game
2. You will need to decrypt the base Japanese CIA. I've started decrypting my files with
rom-converto
3. I recommend making 2 copies of the "PackHack" folder so you can easily copy the contents to the base game
4. Open HackingToolkit3DS.exe and unpack both CIAs using the "CE" command, make sure they're each in their own folders
5. From the unpacked English patch CIA:
a) copy "code.bin" from the ExtractedExeFS folder to the same folder and file of the base game, replace file when prompted
b) copy the entire contents of the "ExtractedRomFS" to the same folder of the base game, replace all files when prompted
6. In the base game folder, open HackingToolkit3DS.exe again and rebuild the CIA using the "CR" command
7. Game should now work pre-patched
Bonus: create compressed cart file for emulators
I don't like installing CIA files when using emulators because of the chaotic nature of 3DS's file system. It's difficult to know where games/updates/DLC are installed and if you're installing full games they take up a lot of space. (some updates and DLC CIA's are extremely large as well) This english patch is fantastic, but the nearly 2GB install size is a bit much, so I like to create more portable CCI files to load easily.
8. Download
rom-converto (skip if you already downloaded in the previous step)
9. Navigate to the "Convert" tab on the right hand pane and drag your newly created pre-patched CIA
10. Run it via "Add 1 to queue" button, it will generate a 3DS or CCI file in the same folder
11. Navigate to the "Compress" tab and drag your newly created pre-patched CCI or 3DS file, once again click the "Add 1 to queue" button
12. It will now compress the game to reduce its size, my final output was 2.43GB.
*note that compressed files (.zcci, z3ds, etc.) only work on Azahar as far as I'm aware