I don't own a 3DS or a 3DS capture card unfortunnately so I am unable to do this properly, but would still love to give this a chance of a run.

Would using the Citra emulator be allowed?

Sadly I don't think so. Citra emulator doesn't have the same framerate as the 3DS and New 3DS, making the final time inaccurate

We have now allowed emulator!