Download the latest versions of Luma3DS and Godmode9 and put them on the spare SD card for the 2DS:
https://github.com/LumaTeam/Luma3DS/releases: Put the boot files on the SD card.
https://github.com/d0k3/GodMode9/releases: Create a folder called "luma" on the SD card, and inside that folder create another folder called "payloads". Copy the GodMode9.firm file from the godmode9 zip file to that payloads folder, and copy the "gm9" folder to the root (main folder) of the SD card.
The 2DS should now boot to a configuration screen with the new SD card, press the START button on that screen. The 2DS should now boot and work normally.
To fix the system not working when there is no SD card inserted, press START while powering on the system, and press A to launch godmode9 from the list. In godmode9, press the home button, select "Scripts..." -> "GM9Megascript" -> "Scripts from Plailect's Guide" -> "Setup Luma3DS to CTRNAND" -> continue, and enter the button combination. Now press B, select "Exit", and power off the system. The 2DS should now work without an inserted SD card.