Pinball missing means literally there is a pinball missing. Or more than 1. There should be 4 balls in the machine, if you have less than this you need to top it up.

That battery holder is nasty. You'll either want to replace it with an off-board battery holder. If you have the right tools and knowledge, it would be even better to get rid of the battery pack entirely and install NVRAM (search on here for Andrew, pinside name Barakandl, he can set you up).

Is there any other acid leakage / damage on the CPU? U19 looks awful, and will need replacement. U16 looks pretty sketchy too. Best to cut out the old chips, then add sockets, then you can just press the new chips into the sockets. Parts are available from Ed at Great Plains Electronics. Read up on the pinwiki guides for WPC maintenance and troubleshooting. It looks like some of the resistors in the area are pretty sketchy too.

Something's not kosher at W16, W17 either. Not sure what these jumpers do or how they should be set, but it looks like something ain't quite right.

Check the installed fuses vs the manual and make sure they are the correct fuses, if someone let the battery pack get that bad, it would not be surprising if they took shortcuts in their pinball maintenance.

Not sure what you mean about the wires and connectors. This one is going to be a work in progress for you, but you're in the right place.

Oops. I was quoting the manual that lists a "install 4 balls" sticker. Manuals are pretty hit and miss for accuracy on stuff like that, I definitely defer to you as you have one in your collection.

Fun fact, I placed an order with GPE this weekend to rebuilt a 7 opto board, a 10 opto board, and a bunch of other stuff. There was a crazy number of wrong specs on parts, I found I had to go to the board and double check all the parts listed because a lot were listed incorrectly.