Also look at the bottom board relays, there might be a loose screw from playfield landed on some relay contacts.

This is a valid point. looking in the pic of the kick switch, it appears there are solder droppings all over, possibly one or more landed on a relay switch.

What circuits run through the empty jones plug at the bottom of pic?

Well it looks like the "extra relay" is being activated by one of lugs from that Jones Plug. when the switch closes, it's making a circuit from the "spare transformer" to the top lug of the Jones Plug to the left of the empty one, and what looks like the fuse holder. It's kinda hard to tell where the other brown wire from the "spare transformer" actually terminates in the pic.