Hey, nice to see another person who had yet to give up on Fates :-) I'm currently in the middle of a playthrough using the patches from the Content Restoration Project, and can confirm they work as intended.
If you are looking to restore Japanese audio, you may also want the Fire Emblem Fates Undub Resync by sataneku. (Mirror for the files available here, since the original link is over a year old now)
From the release description:
"This is to be used with [Team If]'s undub [...] and Luma3ds.
With the undub by itself, in My Room and confession scenes the animations will still be the dubbed version's animations. This hack replaces the dub Live2d animations with the sub ones."
While they said to use it with Luma3DS, this is in no way required - it works the same way as the Undub and other Content Restoration patches, and there are many ways to use them - off the top of my head:
1. You can use NTR with LayeredFS/OnionFS to simply apply the patch every time you launch the game, whether from a Cart, e-Shop download, or legitimate backup.
2. Do the same with Luma3DS' built-in LayeredFS functionality.
3. Build a patched version (if you are already applying the Undub patch, or any of the other Content Restoration patches, you can do them all in one go). While a little more complicated, the result is a permanently modified version of the game, so you never have to fiddle with patch files again.
To do this (sticking to the broad strokes, since the details can easily be found in dedicated tutorials), you need to:
- Create a dump (CXI) of your game cart/eShop-title, decrypt if necessary, extract the ROMFS file, and, depending on what platform you intend to use (Luma3DS, HANS, Citra, etc), the rest of the content, like the ExeFS as well (it depends on what you'll be rebuilding it as).
- Either mount or extract the content of said ROMFS.
- Then, simply paste the files from the patch folder into the ROMFS folder (making sure the folders all line up correctly - you should receive a prompt to overwrite existing files with the same name. Do so).
- Once all the patch files here been properly placed in the ROMFS folder, you're ready to rebuild the ROMFS file. Do so.
- I believe for HANS, that's it - use the last 8 chars if the titleID for the filename, and place it in your /hans folder on the SD. I've only actually used HANS briefly years ago, so I have little actual experience with it.
- For every other option, you'll need to rebuild the CXI; this is where all the other content you extracted earlier is used. Make sure you have all your various and sundry parts (Including the full NCCH and ExeFS headers), then rebuild it.
- Almost done! Now your just need to rebuild the CXI into a CIA that can be installed on a system running CFW. Do so.
- ... And you're done! Banzai! (If you intend to install the game to NAND, you need to quickly encrypt it first).
Note: All of the above I know only thanks to ihaveamac's excellent guide on the subject - check it out, if you haven't already. One necessary deviation from their instructions is to use SciresM's version of the RomFS-Builder, as Fates includes files with Japanese names, which the other options (at least all the ones I tried) can't properly read.
Hope that this post proves to be of some help - I've used the extraction/rebuilding method above to create various versions of Fates while testing, from the CR patches + Undub only, to that + Polygamy mod + Expanded Same-Sex Marriage mod, to CR+UD+Fates-Blade's FEF:Upgraded mod, etc.
It's pretty easy after the first few times - though I recommend keeping a text-file with all the Command-Line commands you run, as if you screw up somewhere, copy/pasting those is a lot easier than retyping everything, and, once you get it right, you can just create a batch-file for extracting, and one for rebuilding, so that any future game patches or hacks will only require a few mouse-clicks.
Anyway, going by this line from the latter part of your post:
"I'm just doing the japanese audio re-dub."
It sounds like you are only looking to apply the Undub, rather than continue where the original Content Restoration Mod team left off. I sadly lack the knowledge to work on restoring things like the Amie system (which seems pretty complex).
With the Fire Emblem If fan translation currently stuck - I believe the biggest still-untranslated parts are the second-generation supports, and all of the DLC, as well as parts of the Invisible Kingdom/Revelations arc (which Harwy apparently translated, but never created a patch for that could be integrated with the fan translation), and no patch existing for the combined Fanslation+Treehouse-for-the-missing-bits version someone built a long time ago, the only hope to get the full experience from the Japanese version right now is to learn to read Kanji - and while my spoken Japanese is decent, my reading/writing is as basic as it gets (Kana + a handful of Kanji) :-(