I'm using Luma, though I don't have either hack working. I have the tools (batch and lunar), and I have the downloads for both hacks. In addition, I did most of what you told me to do, but the game data in the no swap folder in flora has something called "dispos" and "person" and I don't know what those mean. Are they important?
Luma has a function called layeredfs, which is used romhacks by loading modified files instead of the base game files. In order for this to function correctly the folder names and file structure of the modified files has to match those of the base game. Citra doesn't have that option so we have to instead unpack the entire rom, replace the base game files with the modified files, and then rebuild the rom.
To use the gay hack with luma:
Boot up your 3DS Luma’s config menu by holding the SELECT button.
Turn on “Enable Game Patching”
On your 3DS SD card go to “Lumas” folder.
Create a folder called “titles” if there isn’t one
Go to the files you downloaded for the gayhack. Go to the "Luma version" folder and copy the folder with the correct title for your version of fates (look at the readme in the "Luma version" folder) into the "titles" folder on your sd card.
That should be enough to make the gay hack work. Start a new game (not branch of fate) and make sure it is working. Then make a backup in case something goes wrong.
Once you are able to get the gay hack running, you can apply the early flora patch:
In the folder you copied from "Luma version" to your sd card, go to the romfs\GameData folder and find the GameData.bin.lz. Decompress this file with BatchLZ77.
Apply the "FloraEarlyGameData" ips patch to your decompressed GameData.bin.lz
Recompress your GameData.bin.lz with BatchLZ77.
Rename it to GameData.bin.lz if the file name has been changed
Go to the "No Swap" folder in the early flora files and there will be two folders, "GameData" and "m". Copy both of these into the romfs folder on your sd card. When asked if you want to merge/replace files, choose yes to all.
That should make the early flora patch work.
If you want to use the unlock all paralogues patch, it's done basically the same as the early flora patch: decompress your gamedata.bin.lz, apply the ips patch, then recompress the gamedata.bin.lz and rename it if the name was changed.