Below is a mockup I built out of scrap plywood.

Also, your home machine isnt a crowded arcade, where space is money. In the beginning, Arcades would rather have two narrow games, rather than one larger game.
Design with comfort in mind. Nobody wants to feel uncomfortable for long spans, while trying to enjoy something.
And,molex connectors are not designed for multiple swaps. They are tight fitting, and the pins will probably pop out after a bunch of swaps.
Comfort while playing and storage space are both important. I believe the CP is well optimized for both after increasing the spacing from 5-1/2" to 9" between P1 and P2 controls. This was accomplished without re sizing the CP box.
The CP is going to be swappable, not modular. Having a removable CP with LED lights can be very difficult. I plan to build different CPs only after this pedestal is completed. My goal is to have a functional arcade pedestal that can accommodate for that in the future. Currently, the only feasible solution I found is to use encoders that are permanently attached to each removable CP. That would allow swapping to be done with USB cables but the LED power is still molex and I have not found a substitute for that.
Why the IPac2 and PacLED64?
The IPac Ultimate is $1 more, has 96 LED outputs, and includes all wiring harnesses.
I did not notice that a wiring harness came with that deal.
Since it was the same price +/-, I thought having them separate would give me some flexibility in CP configuration.
I now regret that decision after building a mock up. I am afraid that with the (possibly useless) flexibility comes added complexity in hardware and software configuration that I now know is not easy.
The front panel be secured along the back edge with dowels and along the front edge with a latch of some sort.
Dowels were not the best choice. Tongue & groove is a better butt joint.
EVEN BETTER than that would be a 3/4" aluminum C-channel that is glued onto the rear, fixed CP. It sticks out as a track that the front panel slides into it. See attached. I suspect that friction alone will be enough to hold it in place. Once slid into the channel, the front and rear panel will be solidly connected and function as a single piece. Additional C-channel is glued to the front and rear of the CP for aesthetics.
I am still considering
I appreciate the feedback, thank you guys. This is my first arcade build. I know very little, (relatively nothing) about electronics. I was a carpenter for 10 years and wired a 50amp sub panel in my house. I love designing projects and currently use CAD every day at work.