Here's what I did
1) My CP has the typical Player 1 - Trackball - Player 2 layout across the bottom. Across the top I have a 4-way MsPacMan above the player 1 buttons, then 2 buttons for the 4-way and spinner above the left side of the trackball plate, then the spinner above the right side of the trackball plate, then a trigger stick above the player 2 buttons. It works out quite well, and with some modification I could fit additional buttons to the left of the 4-way if I wanted to.
2) You can put the 4-way into a wood panel pretty easily. You will have to take the thing apart (take off microswitches and pull the handle/spring out of the case). Once that is done, you need to route out an area on the top of your CP equal to the max area of the joystick and to a depth equal to the lip of the joystick mounting section. Then, you need to cut out completely a square for the smaller part of the joystick to fit into. You then slide the joystick down from the top and secure it to the panel. The top of the panel should be flush with the top of the joystick. In the Lexan you would just have the center hole for the stick itself. Once you put the lexan on, you can reassemble the joystick and the only height you have lost is the thickness of the lexan.
This may sound complicated, so if I didn't explain it very well let me know.