The first and biggest thing I'd do would be to post ideas here first and do work on them after that. Not only will the people here tell you whether it looks good, will work at all and so on, it will probably lead to even better ideas. I would have saved myself a ton of work if I had done that (I had my reasons for doing it that way, but still).
For the planning part, I wouldn't plan too much ahead. I would do things in order, not worry about something two or three steps ahead. It doesn't make sense planning how to do the monitor hold while sawing the first boards. I wanted to plan everything ahead and ended up overdoing it, planning and worrying and planning and getting nothing accomplished. It also doesn't help that somewhere along the the line you will probably change your design (especially if posting here) and some of the planning ahead time will be wasted.
If I had to build the cab again, I would make it wider so I could make the CP wider. Because of the trackball and the space restrictions it causes, the P1/P2 controls sit a bit higher than intended.
If I had better tools, I would definitely do a front door with a frame for easier access. My plans for doing that without a frame didn't pan out, and I felt that I couldn't cut a perfect rectangle out of a wood panel to make the frame with just a jigsaw / sander.
The only other thing that comes to mind would be using tinted plexiglass for the marquee / monitor, as the tinted lexan scratches really easy.
Oh, one more thing : The Ultrastiks. If I had to buy them again, I would definitively order the stiffer springs also. Since they are analog sticks, they feel really loose.