You will see on the switch matrix that every individual switch has a corresponding row and column pin. For example, the outhole uses 1J8 pin 2 and 1J10 pin 9. In switch test, if you remove both of those connectors (1J8 and 1J10) and short the pins 1J8-2 and 1J10-9 with a jumper or short piece of wire, the switch should show a closure. If it does, the MPU board is good and you have a problem in the wiring from the connectors to the switch, or a bad switch itself. If it doesn't show a closure, then you have a problem on the MPU.
If on the MPU, try to see on the schematic if all of the bad switches go to the same chip. If so, that's probably needing to be replaced.
If wiring is suspect, make sure the switch is good by shorting the wires on the switch itself. If the switch is good, look for a wire which broke free from its solder joint. Switches are daisy chained in the same row and same column so a bad solder on one switch will take out all of the remaining switches down stream.
I find its helpful sometimes to start with the first switch and physically trace the wires to the next switch in the column and the next and so on until you have physically inspected all switches in the matrix. Usually you will find the problem, and its usually a double wire where one of the wires has broken free from its solder joint.