You will need:
1. The latest releases of Anemone3DS (the .cia file), Checkpoint (the .cia file), Homebrew Launcher Wrapper, GodMode9, DSP1, FBI (the .cia and .3dsx files), ctr-no-timeoffset, and Luma3DS Updater (the .cia file).
1. If it isn't already done, power off your device and put your SD card in your computer.
2. Create a cia folder.
2. Copy all .3dsx files into the /3dsx/ folder and copy all .cia files to the /cia/ folder.
3. In the luma folder, make a payloads folder and copy the GodMode9.firm (from the GodMode9 download) file into there.
4. Copy the gm9 folder to the root of your SD card.
You can update your system with B9S + Luma since it is safe to do so. Though, you don't need to right now, since it is all the way up to date.
1. Launch the Download Play application.
2. Press the left bumper + down on the D-pad + the Select button.
3. Select "Miscellaneous options" > "Switch the hb. title to the current app." > Press "B" 3 times.
4. Close and relaunch Download Play.
5. In the Homebrew Launcher, launch ctr-no-offset, press A to set the offset to zero.
6. Press Start to return to the Homebrew Launcher. Then, select Frogtool and select to "RESTORE clean DS Download Play", exit, and then open FBI.
1. Navigate to SD > cia > < current directory > > Install and delete all CIAs
2. Exit Download Play by pressing the Home button and pressing X.
1. Launch DSP1, wait, the press B.
2. Turn off your system, then turn it back on while holding Start.
3. Press A and follow any directions that come up on screen.
4. Press Home to bring up the action menu. Select "Scripts" > "GM9Megascript", "Scripts from Plailect’s Guide", and "Setup Luma3DS to CTRNAND".
5. Follow any directions on screen, then return to the main menu.
6. Finally, to back up, go to "Backup Options" > "SysNAND Backup" > Press A to conifrm - this will take some time, you need 1.3 GB of free space. Press R + B when done and save the output files (in /gm9/out/) to cloud/computer storage, reinsert it into your 3DS and press Start to restart your system.
You are finished! Update your files regularly with Luma3DS Updater and with the Githubs mentioned in this guide.
If you'd like to upgrade your SD card, copy and paste the contents of your old SD card to the new one. If your new SD card is larger than 32 GB, you must format it with guiformat (Windows), gparted (Linux), or Disk Utility (Mac).
For more information on what you can do with a modded 3DS system, go here.
Info sources for this guide: 3DS.guide