PL1/ Scott, thanks for your info. It's starting to make sense to me now.
Ok, so I've been working on the control panel this weekend. Here was my final design that I ended up mocking up in cardboard:

The cardboard mockup was really helpful, because after cutting out the holes and popping in the buttons, joystick and trackball, I was able to see just how much room I have underneath. (Not much!)
Next up was cutting it out of 3/4" plywood.

All the cuts seemed to go very well from the top view:

I couldn't really wrap my head around how to mount the Mag-Stick plus onto the control panel, and still have the CP flush from the stop. After a bit of brainstorming and beer, I routed out the underside of the control panel, to mount the plate.:
Underside View:
I then countersunk the screws, with clocking nuts from the bottom. Now the joystick is connected very well, sturdy and flush with the CP.
Then, I am going to use the mounting plate for the 3" trackball, so I routed out just a small thin layer of wood to get the mounting plate to also sit flush with the CP:
Top view:
Ok, next up was my toughest challenge, and one I was dreading this entire build.
I'm running this MAME bartop off a laptop, and the POWER button from the laptop is one that I had no idea how to make into an arcade button to turn on/off. This "button" isn't really a strong physical button at all. (Have I mentioned I know nothing about wiring? LOL) The button is more like a dimple, firmly attached to a ribbon cable. It looks like this (note this is a different button, not the power button, but just to give you an idea of the style of button I was dealing with):

Well, here, was my completely low-tech stupid idea, that actually worked perfectly. I simply drilling into a switch, and then filled that switch with a hard piece of plastic that will act as a contact point. (unlike a switch, this contact point in firmly in place.) Then, I just trimmed the ribbon cable, while holding it up to the light to ensure I wasn't cutting through any actual wires. I lined everything up before attempting, making a note of exactly where the arcade button's contact point hit that small piece of plastic. Then, the moment of truth: I KRAZY GLUED the button to the laptop's power button onto an arcade button. Now, when you push the arcade button, it touches the laptop's power button, and works perfectly each and every time! It looks like this:

It works!!
Then the last step was to go into Windows XP and set it so that the computer will shutdown automatically when you push the power button.
You do this by right clicking on the desktop and then selecting Properties > Screen Saver > Power > Advanced > "When I press the power button on my computer" select "Shut down". (You can also set it to "Ask me what to do", but then you'l also need an ENTER button on your cabinet to confirm the shutdown. I think I'll live dangerously, and just put the power button in the back.)
This way Windows XP properly shuts down, all via the Power button. It's not a power cut, it's a proper shutdown.
Onto the wiring of the control panel...