Pull the plugs and close the switches right at the header posts. Go row to column and make sure you get just one switch lighting up in test mode.

check resistor networks on those problem pins. See if any look burnt (short to something). Check resistance. Go against the common and the pin on the problem/row column pins. Resistor networks go towards open when failing. Open resistor networks will muck up the matrix.

Next up would be the chips inverting/buffering/isolating the switch matrix signals. probably two 7406s and two 4049s if it is the same as sys 3-7

Nice work Give a really good luck under the PF. Those resistors where good when the board was in my hand. I would assume they burn open when a switch touches something under the PF it shouldnt.