This is pretty cool Kaytrim!
Are you absolutely set on the 'auto' connection thing though?
Reason I ask is that you are going to need a lot of pins in the receptacle ends of the connectors and depending on where you mount it under the deck, all of your modules will need to align perfectly with it. That's going to restrict your placement options a bit. Mating harnes connectors would be so much easer, maybe color code them for ease if identification.
Most of the connections will go unused except for whenever that certain module is plugged in. Some components (I.E. trackball) may not respond well to the 'hot swappable' configuration.
If I understand correctly, you want to use a drop in module board. Could you route out a grove or lip along the inner edge of the hole in the CP deck and have a matching lip or mating surface on the outer edge of the module? If you can keep your tolerances tight they shouldn't move around too much but you'll most likely still end up with a visible seem.
I was wondering if you used magnetic strips along the surfaces of this mating edge, how well they would hold em in place and how likely would they be to cause interference with your controls. You shouldn't need much holding power really. I'm thinking them sheets of 'earth magnet' material, it's very plyable stuff and cuts easy with a scissors. Just not sure how you'd affix it to the modules.

Eitherway I am interested in the idea and look forward to seeing how you work it out!