Quoted from wayout440:

The white/brown and green/red wires are fine. These are your switch row and column wires respectively. There are 2 green/red because the column wire "daisy chains" to the next switch. The oddball is the yellow wire. What's the other end of that attached to? Only switch matrix wires should be connected to switch matrix switches, these are a low voltage digital signal wire. If you ever short any of these (even accidentally coming across them with a tool like a screwdriver) to a power wire such as for solenoids, and the game is on, you will likely blow up the switch matrix - like you did.

Quoted from wayout440:

The white/brown and green/red wires are fine. These are your switch row and column wires respectively. There are 2 green/red because the column wire "daisy chains" to the next switch. The oddball is the yellow wire. What's the other end of that attached to? Only switch matrix wires should be connected to switch matrix switches, these are a low voltage digital signal wire. If you ever short any of these (even accidentally coming across them with a tool like a screwdriver) to a power wire such as for solenoids, and the game is on, you will likely blow up the switch matrix - like you did.

Quoted from wayout440:

If it was wired incorrectly, it would not work correctly. Here is a copy of a section of the switch matrix table pertaining to your trouble area. It looks like your game was rewired with yellow insulated wire as a sub for the green/red column wire, which goes to one side of the outhole, each of the ramp switches, etc. It's ok to leave it as yellow wire, but I would recommend to tag the wire with something, like a tape label with the colors they are *supposed* to be, so that you can keep it straight and make it easier for troubleshooting. Each of those switches will then have a white wire with some color stripe on it going to the other side of that switch (refer to switch matrix diagram)with diode between the row wire and switch with its cathode side attached to the switch.
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Quoted from wayout440:

Trying to get my bearings on what's going on here on your playfield, please bear with me. Your white/X stripe row wires all appear to go to a playfield lug with the diode connected between the lug and the switch, except in the pic attached I can't quite see where the diode is.
The green column wires then can go from the other switch terminals for each switch in that column - in this case green with red stripe. At some point with the absence of having extra properly color coded green/red wire, the chain can continue with yellow wire subbing for green/red for all the switches in column 2 of the switch matrix chart.
It doesn't matter what order you daisy chain, as long as no switches have the exact same grreen/X and white/X wire
Hope that helps.
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Quoted from wayout440:

You have to go through every connection. Point to point. Not only verifying the correct wires, but also nothing is touching something it shouldn't. Check all the switch diodes (if something is wrong with them, that usually won't damage the switch matrix, but make sure they are not touching something else. Preferably install these in clear plastic tubing. )
Check for frayed wire connections. Look for other wires broken or dangling that could touch the switch matrix wires or components. Etc.
When a playfield simply doesn't work and it is original, not swapped, 99% of it is not going to be a problem, simply because most of it is where it was when manufactured. When you swap out and move everything, you disturb the integrity of the original manufacturing and introduce opportunity for error.