The main CPU board goes across the ribbon cables and reads these controls on the SSIO board. Check it systematically by working your way backward:
- Use your DMM on resistance, with the game off, and make sure the switch is closing.
- Enable self-test, test all switches (coins, start buttons, etc) and see what the game recognizes.
- I don't have a tapper pinout, but use your DMM on voltage at the SSIO connector J4 or J5. The line should be pulled to +5 normally then grounded when you close the switch.
- Repeat the same test at the leg of the chip. Looks like B2, E2, and F2 on the SSIO handle the inputs.
- If the switch looks good at the leg of the input chip and the game still doesn't recognize the switch closing, suspect a problem on the buffered data bus.