Yeah there were times I randomly had issues with packhacks a while back, and I have no idea why. As much as it is a great combination of tools, don't use packhacks for this tutorial.
Only grab CTRtool from the link I've provided.
Only dump your game files from your 3DS and grab exeFS from there (I'm under the impression you're trying that with packhacks, else why would you need it?).
Also, make sure you decompress the bin before searching for the values
Because the game uses the code.bin to do stuff. and LayeredFS forces the code.bin you placed to load first.
So let's say the game has v1.4 game files, and other v1.4 instructions to run, but you force it to run a v1.0 code.bin, naturally stuff is only going to partially loaded incorrectly, the game won't have all resources loaded correctly, and won't be able to function. Thus crash.
Pretty much why I specified if you have a game update, gotta use the game update's code.bin..
I experienced the crash firsthand myself, had to guess why it was even happening ><