Luma is recommended, it may work with Soundhax + Fasthax, but it's untested.
How to use Rom-Kit from kit-kat to Extract/Rebuild .3ds and .cia files
Step 1 - SD Card Setup
- Get Decrypt9 and extract the Decrypt9WIP.bin file to "sd:/luma/payloads" and rename it to x_Decrypt9WIP.bin,
- Put your .3ds/.cia backup into "sd:/files9". (Create it if not already there),
- You will need the following files: "seeddb.bin", "slot0x1BKeyX.bin", "slot0x05KeyY.bin", "slot0x11key96.bin",...
How to use Rom-Kit from kit-kat to Extract/Rebuild .3ds and .cia files