Sounds like you got a bunch of connector issues buddy. Not the settings.

Check all the connectors, including the loose molex and the crimps over by the big can capacitor, and make sure they are all in the boards and each other nice and firm. You'll probably have to replace some in the long run.

You Posted this in the EM Tech Forum,
You need the Solid State Forum.
Great Machine!

It sounds like something shorted when you changed the batteries. One of the transistors or SCRs might be bad. Do you have a manual / schematic for the machine? If not, there is one available on IPDB;

http://mirror2.ipdb.org/files/871/Williams_1979_Flash_Manual.pdf

As phil-lee mentioned, post this issue in the Early Solid State forum and we'll meet you over there with some more suggestions:

https://pinside.com/pinball/forum/forum/tech-early-80s-solid-state

If the lamps under the plastics are out those are GI general Illumination. The lamps under number inserts are CPU controlled. Looks like those are on and if dancing in attract mode is a good sign.

Do you know what system board you have 3-6? Yellow flipper roms or Green? As setting in adjustment handbook changed depending on the color.

Post a picture or two of the boards.

Check all fuses for proper value and continuity with a digital multimeter.