That's pretty nice... I'm triying to do the same but I have some problems...
Once I edit the decrypted romfs.bin (using GARC Unpacker, XYText & XYEWE)... I use Makerom to get a new Romfs.bin, then I use this command:
makerom -f cia -rsf exefs\cia.rsf -target d -desc app:4 -o Pokemon_X.cia -icon...