Hi!
According to https://www.retrode.com/plug-in-adapters/ the N64 cartridges should be 3.3V. I do not own an N64, but is it possible to remove the cover of a cartridge and stick only the PCB in the console? If so, you could measure the "original-voltage" there... Just to avoid the magic blue smoke thing you know... 
I did not have a look at the current sourcecode / the N64 parts, but maybe some output via serial or using e.g. an Atmel ICE (looking at the variables) could also help to debug the steps of cartridge detection?! If you need help there, feel free to PM me.
Truely impressive, what all you guys did here - it is hardly comparable to the tiny project I published three years ago... 
Best regards,
Michael