I did manage to achieve that (involves just changing a simple pointer), don't remember if I took notes & don't have access to my PC right now. I'll try and post my notes later this week (no guarantees though, I've been quite busy IRL these past couple weeks and haven't even had time to work on my FFII retranslation).
As for the 3DS color palette patch, yeah I know I said back in June that I'll gladly do it but I'm satisfied with the NTSC replication patch. I can provide the offset though, and it's a really easy patch to make as the whole game only uses 64 (or possibly even less) colors. Another thing is if it's worth my time to do it, as I have little time these days that I would rather not sacrifice.
I tried to reverse engineer the IPS patches.
I managed to find the pointer.
It's as 0x1F0.
The original pointers is A5370108, which is a little endian pointer that goes to address 0x0137A5.
Your autoboot hack has that very same pointer changed to points to 0xF000F0.
The pointer is in little endian is F000F008.
I tried to debug the game to see what address the game uses to go to Mother 2, but I didn't have any luck at all. :/
Do you have a method to do so? And what tools did you use?
If you could explain me via PM if you want, I would be really thankful, since I want to do the same for the Super Mario Advance series to boot straight into the main game and knowing how to do so will come in handy.
Apart from that, for anyone that wants to make the 3DS colour patch a thing, here you have the offset range for the Mother 1 palette.
Mother 1 Palette Data BankF6441C-F64497