Yuu should only have to inspect the switches in row 4 to make sure that the white/yellow wire isn't grounded or broken off and touching ground. There are only 6 switches in that row as SW24 is nothing more than a diode on the coindoor interface panel, but you should still inspect the wires at J1 and J6.
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No, If you fried something on the board, the ground short would likely remain when removing the row connector. Did you remove only J212, or J209 as well? When I read the post I was was thinking you removed both the playfield and cabinet connectors; if only J212 was removed and J209 was still in place and the this changes things a little and moves the potential location to the cabinet as J212 goes directly to the coin door interface board for the cabinet switches.

Other thoughts: Its also possible that the ground short remained with J212 removed and was not seen due to the "Check Fuses" error. The best thing to do is go into switch test to see if all of Row 4 is showing as closed or not.

I don't see how it would be related.

Just for clarification, can you post a picture of the switch matrix with J209 removed and another with it connected?

If Row 4 is the ONLY row that shows all switches closed across the row, then somewhere one of the White/Yellow wires for row 4 is pulling the row low all the time.

I suppose its also possible that the column 2 pulse could be stuck low all the time, if this is the case it would drive Row 4 low all the time through SW24. This is very easy to test, while in switch test if you close the coin door, only SW22 should show a closure, if all of Row2 closes you likely damaged U20 on the CPU board.

If you have a logic probe, the point of test is U20-17, or pin 2 on CPU headers J206, J207, and J212.
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These are direct ground switches and connect to J205 on the CPU board, make sure this cable stays connected.

Your connector for the direct ground switches is off by a pin, you may want to correct this.

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If you have a ground short in row 4 with J209 removed as shown in post 26, this problem is NOT caused by anything on the playfield since you disconnected all the row wiring from the entire playfield and the problem remained.

I'm trying to make diagnostics of this as easy as possible.

What does the switch matrix look like when you have the coin door closed?

I agree...Or just replace them with AA lithium batteries you wouldn't want bad things to happen to such a pristine looking board.

This alarm is caused by a failure of the switch matrix, you can measure your +12VR at TP3 on the power board to make sure its there as this is the voltage that powers the switch matrix. I can't recall if the logic for this alarm calls for all switches in the matrix to read open or just Switch 24; earlier you got this alarm by removing J212, so I assume its the later.

If removing only J209 clears the ground short than yes, the issue is on the playfield.

I would be worried taking it anyone that isn't familiar with working on these old boards with tiny traces. I've seen work from repair technicians that made me shake my head in disbelief. You are better off taking it to someone familiar working on these boards, if they aren't capable of testing the entire switch matrix with the board out of the machine I wouldn't even think of letting them touch it.

You just never know .... This board was "repaired" by a "competent technician" who was absolutely sure it could repair it:
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This is what it looked like under the chip:
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The damage is done when removing the original IC, so yes.

You mean like this?:
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A board repair tech should be able to remove the IC, socket the board, and reinstall the same chip that was removed into the IC socket have have everything work when powered on.

Sorry, I totally derailed this thread.

The fuse in the damaged holder is for one of your GI lines, completely unrelated.