Over the weekend I got a few more things done. After successfully mounting the controls on the sample panel, I spent some time marking out where the holes and cuts should be made in the actual panel. This was a bit strange since I marked everything on the underside of the top panel, so it all had to be mirrored.
In addition, I got the slot for the T-moulding routed in the outside edge of the control panel. I ordered a bit from Rockler to do this and it did the job perfectly.
Tonight I'm going to recheck the layout on the control panel and then start cutting the holes for the buttons, joysticks, and trackball.