What game/region are you using?
EDIT: Actually never mind. What you need to do is rename your REBUILT Romfs file, depending on the game you're using. Here's a list of the games (all capital letters are important!)
OR - 0011C400.romfs
AS - 0011C500.romfs
X - 00055D00.romfs
Y - 00055E00.romfs
After that, you need to do is download HxD (google it) and follow STEP 6 of this tutorial.
http://wololo.net/2015/10/28/tutorial-hack-pack-3ds-rom-use-hans/
Then after that you need to go into the exefs/exe/exedir folder (whatever it's called, the one that pk3ds is directed to), and change your .code.bin file similarly to the romfs file above. Rebuilding your Exefs doesn't have anything to do with this, ignore that.
For example, if you're changing Omega Ruby, you'll want to name your .code.bin file to 0011C400.code (yes, you're changing the file to a .code).
After that I think you can just stick those two files (0011C400.romfs and 0011C400.code if you're playing Omega Ruby) in your SD card and you're good to set up the game with Hans or whatever it is you're doing.
If you need instructions on that, too, then here:
1. Make a folder on your SD card root called Hans
2. Put your .romfs and .code files into this folder
3. Put your SD card back into your 3DS and start up homebrew and Hans, choose your Pokemon game and make sure the cartridge is in
4. Change the Code -> SD and Romfs -> SD options to yes
5. Hit OK, play the game
Hope this helps, and I hope I didn't phrase any of this in a confusing way.