Couple things to try/check out:

Put the game in switch test, then remove connectors 1J8 and 1J10 from the MPU. Take an alligator jumper and clip it to the first pin on 1J8, then use the other end to touch each pin on 1J10 one at a time. That will simulate the switch closures for the first column of switches. Watching the displays, you can verify whether each switch is being detected properly at the MPU. Once you've tested all the switches on column 1, move the clip to the next pin on 1J8 and run down the same procedure. If everything works properly at the MPU, you'll know it's a playfield issue.

Another thought: a lot of times, switch matrix problems like this can have a pattern. They often make a square or rectangle on the switch matrix chart when there's an issue with a stuck/shorted/mis-wired switch or diode. In your case, the switch that's standing out to me is the "playfield tilt"... Acting as a 'corner' it makes the 'rectangle' with the other 3 switches related to the problem. See here:

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So my suggestion would be to verify that the playfield tilt switch wiring and diode are correctly oriented (make certain the wiring is correct, no diodes backwards or wires going to wrong lugs, make sure tensioner blades on the switches aren't causing shorts across the switch blades, etc), and make sure the switch itself isn't stuck closed somehow. Verify those same things at *all* the other switches on columns 2+8. Also note the flipper switches referenced in Column 8 are the low-voltage switches attached to the flippers (not sure if they're on the flipper mechs themselves or stacked on the cabinet flipper buttons... They're used for the lane-change feature)

Switch 57 and 58 (flipper switches) are the 4N25 optocouplers on the Interconnect board. They are NOT physical (leaf or micro) switches.

Switch 59 (Magna Save(tm)) is a leaf switch in the cabinet.

Excellent! Glad you found the culprit and fixed it. Thanks for following up with the solution!