How to eliminate this mess...
Well, one step at a time.
Where we live as people who restore pinballs is in the middle of the question "how far do I go?"
Addams are worth the time and money, but I'll tell anybody that Addams have problems you don't find on any other machine. They get worn out in ways you don't see on any other pinball. Thus any Addams restoration is going to be a legendary amount of work relative to most any other restoration you do.
How far do you go?
Personally, I would pull the playfield out of the box, pull everything out of the bottom of the game and clean the wood and paint the inside of the box first. I'd put the metal power input box in a metal polisher after removing the german sticker and get it shiny. I'd replace the MOV just because I was there. Fresh ground strap. Fresh power cord. This restoration is worth the extra work.
I was watching a shipbuilder who was instructing new apprentices, and they put some braces in, some of them long, some of them short. He made them cut every brace to exactly the same angle... not because it mattered, but because he (and they) were going to be spending a lot of time working in the boat environment, and if you surround yourself with things done RIGHT you are constantly reminded to do the right thing.
So... a clean bottom box with a fresh coat of paint sets the tone.
Power into the transformer is wired correctly! So cut out the splice to the brick power supply, and cut out the wires that the brick power supply had running to the CPU.
My friend James told me early in my career that the single thing you can do that gives the greatest appearance of professionalism is to keep it clean. So keep it clean. Wash the wires, get the dirt and dust off them. If it's ugly, replace it with something beautiful.
While you are looking at the power in to the game and the power box, I would run another outlet to 120v AFTER the power switch. (The soldering iron power plug currently on the power box in the bottom of the game doesn't cut off when you shut off the power switch.) I like to power mods with a separate power supply, and having an outlet that cuts power off when you shut off the pinball will be helpful. It looks like somebody has put a mod into the 12V coming off the power board. Best practice... don't strain the 30+year old power board 12v supply with mods.
Other than that, you have 30+ years of ham-fisted technicians doing really wrong things here. You are going to be revisiting every single thing that they have messed up.
One step at a time.
So... how to eliminate this mess:
Get a clean work environment.
Start at the wall plug and consider replacing every single thing you come in contact with.
You are going to be living in the middle of the question "How far do I go", so be thinking about this both on a small scale (should I replace the pins in this connector?) and a big scale (should I replace the playfield and rebuild the entire wiring harness from scratch?).
Work harder than you think you should.
Put more money into it than you should.
This rebuild is going to be one of your 'legendary' accomplishments, and you only do a limited number of projects this scale in your entire life.
Make it worth it.