I'm not generating a constant clock signal on that pin, it just pulses the clock shortly when it's reading/writing. Also the clock signal is just needed for eeprom save games. So even without it all other save types should still work.
What game(s) are you trying exactly?
What exactly is happening when you try to read save games?
It could be that your wires are just too long, since I never tested the code with anything else than my pcb.
Does the n64.txt get read from the SD card correctly so that it shows the right save type for the game in the oled screen?
Do you run your Arduino with 5V or 3.3V?
Do you have the S_Dat pin(n64 cartslot pinout) connected to pin 7 of the Arduino and with a 1K resistor to VCC? It's needed for eeprom saves.
Sometimes it's good to play the game shortly in a real console before dumping with the cart reader.
I think it's best to wait for the pcb's to arrive, so many thing that could be wrong and at the same time maybe nothing is wrong and you just found a bug in my code 