Try updating the system from system settings or recovery mode. If it still crashes after updating it, backup your games with
GodMode9 and saves with
Checkpoint and All the data that's on your sd card, and do a system format. Put everything back to the sd card after doing that. Don't let it create a new Nintendo 3DS folder, make sure to put yours before you boot the system.
And if you want to use new Luma3DS & GodMode9 files, get them from
here and put them on the sd card instead of the ones that you have.
No, you shouldn't uninstall cfw on your system at this state, and it will only make it worse if you do so.
If the above doesn't fix it, then you might have to do a
CTRTransfer. Follow the steps carefully, and keep your game and save backups because you'll need them..