128 outputs, 128 inputs with pullup resistors.
Read all inputs, make sure none shorted to Gnd/shield/backshell.
Drive 1 output low, read all inputs and check that only the correct one is going low.
Confirms continuity and no shorts to other pins.
Bank of shift out registers and shift in registers, all daisy chained.
I would use open-drain shift out registers to sink current from the pullup resistor, won't be damaged by shorts.