Also, the metal trackball mount plate sticks up about 1/16" to 1/8" from the surface of the wood. Will the lexan be ok to cover that or will it look weird being uneven?
To make it look nice, you should route out the wood 1/16" so the top of the plate is even with the top of the wood. A router would be the easiest to do this with obviously, but you could chisel it out. Plywood would be the easiest to chisel.
Here's how I'd do it with a chisel: use the cutout template on the wood and mark: the cutout for the TB case, the four holes in the corners to hold the plate, and the outline of the plate. Cut the cutout. Drill the four bolt holes for the plate, slide the plate onto the CP, and check the outline. Redraw the outline to the actual plate edges if different. With a chisel, cut straight down along the whole outline (don't worry too much about going too deep, but be sure to go at least 1/16" down). Chisel from the inside toward the edges, being careful around the edges. Go slowly, checking the depth by sliding the mounting plate into place. It doesn't need to be absolutely flat, but closer you can get it to flat, the better. Chisel or sand as needed.
After done, screw in the plate, fasten the lexan to the board, put a piece of wood on the other side of the lexan, and use the hole in the mounting plate to guide the hole in the lexan. (much others suggested cutting the lexan)