Before going big, make a singular noticable change.
Then make sure packhack is recompiling the files that pk3DS touches and edits.
If you have doubts, get packhack to re-decompile the ROM that was recompiled, in a different spot, then open it up with PK3DS to confirm the change is there.
Then, when you're happy that the change is indeed there, get Citra to run the game.
Something has to be wrong with one of your steps, gotta figure out which one it is.