If a custom keyboard is installed and custom firmware is removed from the console, System Settings will be inaccessible and you will not be able to launch the keyboard. This is obviously detrimental to the overall functioning of your 3DS and should be fixed as soon as possible.

Unbricking a 3DS with a custom keyboard installed

If Internet access isn't currently set up, you can set up an Internet connection from Safe Mode as the keyboard will still work there (hold L+R+↑+A on boot, then follow its prompts).

Methods that require additional hardware

The following methods require extra hardware but is the recommended way of recovering from this as they should work 100% of the time regardless of system version:

ntrboot (Requires a compatible flashcard)
kartdlphax (Requires a second console and a copy of Mario Kart 7, both the same region as your console))

Methods that don't require seedminer

The following methods do not require seedminer and can be followed like normal:

super-skaterhax
basehaxx (Pokémon Omega Ruby/Alpha Sapphire on cartridge)

Methods that require seedminer

If you have a copy of any of the following:

Your NAND backup (e.g. 220101_AA000000000_sysnand_000.bin)
essentials.exefs
movable.sed

YOU DO NOT NEED TO MINE YOUR SEED AGAIN.

For instructions on extracting your movable.sed from your NAND backup or from essentials.exefs, see this page.

Section I: Installing Pokémon Picross

If the eShop requires you to use the keyboard, or you cannot install Pokémon Picross, there's no point following the rest of this guide and you should choose another method.

Follow these steps to redownload Pokémon Picross if available

Section II: Mii mining

If you already have your movable.sed, you can skip this section.

Because you can't enter a friend code due to the broken keyboard, you'll need to get your console's encryption key a different way. We can accomplish this by Mii mining.

Follow Mii mining to extract the movable.sed from your console, but do not continue onto the main guide as it suggests. Come back to this page once you have the movable.

Section III: PicHaxx

Now that you have your movable.sed, continue to Homebrew Launcher (PicHaxx).

Section I: Installing Steel Diver: Sub Wars

If the eShop requires you to use the keyboard, or you cannot install Steel Diver: Sub Wars, there's no point following the rest of this guide and you should choose another method.

Follow these steps to redownload Steel Diver: Sub Wars if available

Section II: Mii mining

If you already have your movable.sed, you can skip this section.

Because you can't enter a friend code due to the broken keyboard, you'll need to get your console's encryption key a different way. We can accomplish this by Mii mining.

Follow Mii mining to extract the movable.sed from your console, but do not continue onto the main guide as it suggests. Come back to this page once you have the movable.

Section III: Steelhax

Now that you have your movable.sed, continue to Homebrew Launcher (steelhax).

Section I: Installing Mario Kart 7

If the eShop requires you to use the keyboard, or you cannot install Mario Kart 7 or its 1.2 update, there's no point following the rest of this guide and you should choose another method.

If you have a cartridge of Mario Kart 7 and it's the same region as your console, you can skip this section.

Follow these steps to redownload Mario Kart 7 if available

Section II: Updating Mario Kart 7

Follow these steps to update Mario Kart 7

Section III: Mii mining

If you already have your movable.sed, you can skip this section.

Because you can't enter a friend code due to the broken keyboard, you'll need to get your console's encryption key a different way. We can accomplish this by Mii mining.

Follow Mii mining to extract the movable.sed from your console, but do not continue onto the main guide as it suggests. Come back to this page once you have the movable.

Section IV: Kartminer7

Now that you have your movable.sed, continue to installing-boot9strap-(Kartminer7).

If everything went well, you should end up with boot9strap installed and the keyboard / System Settings should work again.

Do not uninstall custom firmware again without guidance. You've now seen first-hand how it can go wrong.