I spent my last few months porting Quake 3 Arena to most consoles that didn't have a port yet (Wii, PS3, PS4, Xbox One), but my main roadblock was always the Wii U. Thanks to all the experience I gained from my previous ports as well as a new toy...
I wonder if it would be possible to reuse GodMode9's free space calculation (which is noticeably faster than Nintendo's code) during pre-boot, disable Nintendo's from running, and write the correct value in memory where Nintendo's would.
3DS Cartridge Fixer Tool
Feel free to use the cartridge fixer if the above did not make the cartridge verify successfully.
Download
Usage:
Install Luma CFW if it is not already installed.
Download the compiled .firm file from the Releases...