I've got A9LH and Luma on my 3DS too, never had any problems with the method in the installation guide; it also worked with rxtools. Maybe your tutorial will shed some light on what the problem is.
The trainer party documents are in progress, I've just been busy with uni lately so they haven't been worked on in a while. I'll try to get them finished and uploaded some time in the next few weeks, once my exams are over.
Still can't figure out why changing the GameID is still a problem. Credit to Asia81's tutorial on
how to decrypt, extract, and rebuild 3DS ROMs and
AuroraWright's info on Luma3DS.
Tutorial:
Things needed:
-A 3DS with A9LH/Luma
-A .3ds of Pokemon X/Y
-Decrypt9WIP
-Asia81's PackHack
-Simple 3DS to CIA Converter
1) Extract all archive files to their own folders.
2) Obtain a .3ds of Pokemon X and Y. I personally use Uncart with a Y cartridge, which can be loaded by holding X on boot.
3) Turn off your 3DS and place its SD card into your PC.
4) Check if you can run Decrypt9WIP through homebrew. If you can, put the 3DS's SD card into your PC and skip to step 7.
5) Take the Decrypt9WIP.bin out of the Decrypt9WIP folder you extracted and place it into the luma\payloads folder. The luma folder should be on the root of your SD card.
6) Rename it to up_Decrypt9WIP.bin. You can use other combos as well, I used Up because it's convenient. Check AuroraWright's page that I linked above if you want to do so.
7) Create a folder named Decrypt9 on the root of your SD card.
8) Take your .3ds of X/Y and place it into the Decrypt9 folder. If you used Uncart, it should be on the root. Rename it to something like PokemonY.3ds, just no special characters.
9) Put the SD card back into your 3DS and run Decrypt9, whether it be holding Up on boot or homebrew.
10) Choose
Decryptor Options, then
NCCH/NCSD Decryptor.
11) Wait for it to finish, grab your .3ds back from the Decrypt9 folder and place into your PackHack folder.
12) Install PackHack if you haven't already, then type in D. Follow the instructions. It doesn't matter if you decompress the code.bin, there's one provided already.
13) Follow regular instructions on Pokemon Eternal X and Wilting Y. Delete the code.bin that PackHack gave you and use the one that's provided. Do not copy the icon.bin over. Make sure you place that .CRO file into the DecryptedRomFS folder.
Side note: The icon that PackHack gives has a different file format to the one you provided. There's also a banner that's in there unlike using Braindump.
14) Go back to PackHack, type in 3DSB, point the program to the respective DecryptedRomFS folder, the DecryptedExeFS folder, and Pokemon Wilting X and Y's DecryptedExHeader.bin.
15) Save it into the roms folder of Simple 3DS to CIA Converter. If it asks to compress the .code.bin, say yes.
16) Load Simple 3DS to CIA Converter and turn the .3ds into a .CIA, install with preferred means.