You may have a shorted bridge rectifier. Did you test all rectifiers on the driver board?

Then it likely points to a board failure. What makes you think it's a connector plugged in wrong?

J101 is connected properly in your photo. Most connectors, including this one, are keyed to where you can't plug them in wrong. The problem is somewhere between the transformer and filter capacitors for the rest of the game. It's got to be a shorted rectifier, they will fail intermittently before shorting out. I'm concerned this happened at all, aren't there supposed to be fuses between AC power and the bridges?

Looked at your photo again and holy crap, looks like you header is a 7 pin and your connector is 8 pin! And it's not a keyed connector, because connector pins are present in all 8 positions. Someone who had the game before you fixed it improperly. Looks like you may have plugged it in one spot over and shorted the blue wires to a common trace. No fault of your own, but situations like this are why technicians need to do a fix correctly so it won't cause problems for future owners.

You're lucky if you didn't melt the insulation on that wire harness. You're also lucky if you didn't damage the transformer...

I would get a second opinion on that connector. It's a standard AC secondary input for WPC-89 machines. The connector (and possibly some wiring, if not the transformer also) will have to be replaced with a properly configured and properly keyed 7 pin connector. And if the short caused heat damage to the header pins on the driver board, that header will need to be replaced as well. You have two 9vAC windings coming from the transformer. The blue one is shared across 4 pins, the red one is two. With the power off, check for ohms resistance on a meter between the two blue wires, then between the two red wires. Tell us what the meter reads. Do this with the connector removed from the board.

Yes, but neither of us know how it should be connected. I would strongly suggest you don't until someone posts a photo and you're absolutely sure the pins/wire colors are in the correct positions.

Perfect! So the key is the spot between the red and blue wires. If your transformer test is good (not a resistance reading of zero on either winding) then I would say you're safe. Line that spot up with the missing pin on the board header with the topmost pin hanging over, plug it in, and turn it on.

You will be good to go if the transformer windings test fine.

Dang, I was hoping they would be good... I wonder if you can scrape the pins down with a blade enough to test for now?

Great, glad it works. Just may give you reset problems down the road due to a compromised connection. As for the initial problem, there is probably an open/bad diode on your upper or lower right flipper. Do you know how to check those?

You will also get heat buildup at this connector which will eventually do more damage.