Hi guys I have a stern freefall here that is giving me a hell of a time with the switch matrix. So far what has been done is the following:
Connector J3 has been repinned and wire colors double checked
Every Switch capacitor has been cut
Every diode has been replaced
The coin door harness has been unplugged
The pins for rows and columns on the alltek board have been jumpered to test the board itself to test and the ones I did worked fine

So the symptoms are as follows:
Switch 2 activates 1
s4 activates 3
s12 activates 11
s14 activates 13
s18 activates 17
s20 activates 19
s26 activates 25
s28 activates 27
s33 activates 25
s34 activates 26
s35 activates 27
s36 activates 28
s37 activates 29
s38 activates 30
s39 activates 31
s40 activates 32

The only thing I can think it might be would be a problem with the wiring harness

Ok, good news. By removing the wires from that connector 1 at a time and found that if I removed the white-yellow wire, many of the issues went away. So I inspected the switches on that wire closely and I found the issue. The top 3 standup targets have lightbulbs directly behind themn one was not screwed in all the way, I unscrewed it and left it hanging in the air for testing purposes and that seemed to fix the problems with the switches that were 8 apart and activating both. Now our issues should be limited to the following switches

Switch 2 activates 1
s4 activates 3
s12 activates 11
s13 activates 12
s14 activates 13
s18 activates 17
s20 activates 19
s26 activates 25
s28 activates 27