A few links to Nintendo 3DS firmware. The first tweet below hints of Nintendo having a response (ban?) to custom firmware.
sighax is a BootROM exploit (revealed at 33c3) for the Nintendo 3DS/2DS/New3DS. It exploits a vulnerability in the RSA signature parser and allows you to run fake-signed firmware on any console.
“Keyshuffling Attack for Persistent Early Code Execution in the Nintendo 3DS Secure Bootchain”
A complete guide to developer 3DS custom firmware, from stock to boot9strap.
A tool to parse, extract, and builds 3DS firmware files
Luma3DS is a program to patch the system software of (New) Nintendo 3DS handheld consoles “on the fly”, adding features (such as per-game language settings and debugging capabilities for developers) and removing restrictions enforced by Nintendo (such as the region lock). It also allows you to run unauthorized (“homebrew”) content by removing signature checks. To use it, you will need a console capable of running homebrew software on the ARM9 processor. We recommend Plailect’s guide for details on how to get your system ready.