Thank you so much for the replies. I finally had some time to mess with things, so here are some pictures:
Here is the control panel:
Feel free to make fun of it

I made it with the following in mind: I wanted 4 players and I wanted a trackball for Marble Madness, Capcom Bowling, etc. I also wanted a spinner for Arkanoid. So it will accommodate all of that. Why I gave the 3rd and 4th players 6 buttons, I have no idea. I know I had a specific reason in my head when I first started this 7 years ago, but it was such a long time ago I forgot why. I am hoping my posts jar my memory.
The one major issue I am having is figuring out how I am supposed to cut plexiglass so it matches perfectly with the control panel I built? I am assuming that is what most people do, right? Cut the wood and holes, lay down some artwork, and then put plexiglass on top to seal it shut? I have no clue how to cut plexiglass without it getting destroyed. Especially the spot for the trackball.
Anyway, I got everything up and running as my ArcadeVGA came in this week. And here is where I am further confused.
Well first off, everything works OK:
I doubt you can tell from the picture, but the picture does not seem to be as bright as I think it should be. I did mess around with every single pot on the back of the monitor, including the two that are off by themselves (labeled “focus” and “picture”), and I messed with the brightness on the back of the monitor and the little control board that attaches to the screen as well. I got it the best I possibly could but the picture still looks a bit darker than I expected and not as razor sharp as I had expected as well. I made sure to tell MaLa to run at 320x240 so I am not sure I am doing anything wrong. If anyone knows what could be up, please let me know. I am really, really paranoid about this monitor ever dying since replacements are literally impossible to find.
Anyway, there’s a few more things I am confused about. One is this thing. I made this for my MAME cabinet and I don’t remember why:
Don’t mind the mess of VHS tapes in the background. I have a bit of a hoarding problem.
Anyway, what possible use could I have had for this wiring thing I made? It looks like my plan was to power something in my MAME cabinet by using the PC’s molex connector. But I cannot for the life of me remember what. I know how silly this post is; asking people to help me remember why I did certain things. But with such a gap of when I was finally able to restart this, my memory is hazy.
Also, I have an LED-WIZ and a J-PAC. What is the 3rd thing I need so I can actually hook all these buttons up? I am assuming with these two (LED-WIZ and a J-PAC) it’s not enough, right?
Thanks so much for taking the time to read my dumb questions. I feel like I have amnesia and I am trying to remember everything I did and why.