Nice design! Make sure you leave enough room underneath for the switches, as I fail to do pretty much every time. Is the big square in the centre for a trackball? I really struggled with the layout for the new control panel for the machine at the space. It was tight to squeeze three more buttons in per player. I think I have it, but we'll have to see if it affect playability.
Do you bother to route out a space for the mounting plate for the joysticks? I'm using 3/4 plywood, so I think I'm going to have to route out 1/4" or so to get the proper joystick height...
What do you do with the keyboard mouse? I've also cut a new front piece for below the control panel (the one that was in there was pretty rough). I'm thinking about installing some sort of sliding drawer if I can find some rails that are low profile enough.