Sorry for the delay , I was out playing disc golf past few days. U1 is definitely bad. You mention J3 pin 5 being at 1.2 volts (MPU sees this as ground) J3 pin 5 is what connects R1 (Row 1) and not switch #35 (the 3 comes from pin 12 of J3 , which is Column 3 , the 5 comes from Row 5 , which is pin 9). As you measured , pin 5 (row 1) always remains at 1.2 if J1/J2 are connected or not. This means that what ever the voltage that appears on pin 10 of U1 , it's output , pin 13 never changes states from HIGH (12v) back down to ground (0v). It always remains really close to 0v, so the MPU sees row 1 closed all the time.
Now , the fact that pins 8, 9 and 10 (Rows 4,5 and 6) are at 1.2v when J1/J2 is connected , but come back high once disconnected,would actually mean that Optos 4,5 and 6 are permanently sending a low signal to connector J2 pins 4,3 and 2. The opamp reacts properly and when it sees these 3 optos grounded , it sends a ground signal through its pins 1, 13 and 2 towards the MPU.
So as it is , it seems that J2 is sending ground signals over pins 4,3 and 2 constantly , which the opamp interprets as closed switches , and sends a ground signal over J3 pins 8,9 and 10.
I'm sorry I had not been more precise. Remember this : You use diode test , to test a diode! (Most of the time). It can also be used to test continuity (you would read 0v for a short , and not OL (overload). The last test you use diode test for , is to test transistors as they are made of diodes in a specific way (in theory, reality is a tiny bit different than diodes). So diode test = Diodes, Transistors , continuity.
Everything you will measure on the opto board is in DC voltage. (2 lines with one dotted).
Plug back in everything , set your meter to DC volts , turn on the machine , and write down the voltage measured at these pins :
U1 pin 10 = ? I assume this pin will be at 12v. It should drop to 0v if the trough jam is detected. You should be able to see this voltage change when you block the trough jam opto with a finger or paper to block the IR from reaching the sensor. The output of this opamp (u1 pin 13) is stucked low. It needs to be changed (install a socket when you remove the chip).
U2 pins 6, 10 and 4 = ? I assume you are going to measure something really low. 1.5v to 0v or close.
Measure once again but at the connect J2 this time :
J2 pins 4,3 and 2 = ? Should still be low , and should be the reason why rows 4,5 and 6 are grounded.
If this is the case, you now have a few choices on what to do. You can , take a known working opto , like trough 2 (sw #33) and exchange it with a suspected broken opto. If you no longer have that replaced opto as a grounded row where you installed that opto , but the trough 2 now gives you issues , then this means you've move the bad opto to a once working switch , confirming the opto is broken.
It is weird that 3 optos would fail all at once (possible if a problematic voltage was applied to the optos , but chances are that would of caused the same issue on ALL optos. This seems to point to a short circuit in your playfield , possibly a pinched wire from lifting the playfield or something.
Disconnect J2 and power on. Are rows 4,5 and 6 still shorted ?
** The only pattern-breaking one is U1 pin 13 (again this corresponds to SW 35--trough 4). **
You were on diode test (which can test short circuits) and you had one probe on the ground. Measuring pin 13 with diode test showed you that there was 0v between pin 13 of U1 and the ground, meaning there is continuity between pin 13 and ground. (you have just confirmed U1 is shorted at pin 13)
Confirm that J2 as its 3 pins low (4,3 and 2) by measuring DC voltage between ground and each pin. Unplug J2 and measure the same pins but on the opto board, are they still low ? Or do you measure closer to 12v ? If they are no longer low with J2 removed, you've confirmed that J2 is grounding those 3 rows.
Pay attention to the wires connected to 4,3 and 2 and look for anything suspicious , damaged insulation , wires running behind something you can't properly see, etc.
If there are no short circuits , swap a known working opto with a suspected one.
Like you tested the switches with a diode directly on the MPU board , a similar test can be done. Disconnect J2 and use a wire (doesn't need to be a diode) between ground and pins 4,3, 2 of J2, the output at J3 pins 8,9 and 10 should change high (12v) and low (0v) when you are grounding pins 4, 3 and 2 of J2.
**Switch 24 should always be closed, switch 51 , cube position 1 , would make sense if the cube starts in position 1. Those 2 switches seem very normal.
So far , U1 needs to be replaced, now we need to find out what is grounding pins 4,3 and 2 of J2. Is it the optos themselves, or a short circuit on the wires.