Hi KungFuJoe,
Have you thought about a modular or swappable panel to avoid what you described as "frankenpanel"? Modular is great if you have to "have it all". I wouldn't have done it any other way. Well, I did have swappable panels at first but I really needed to have *it all*. 
~telengard
Me too, except that I DID try the frankenpanel first, then went swappable, then went modular.
Another nice thing about modular is that it will let you swap stuff from one cabinet to another, which is where I'm headed soon.
I converted my existing cab to vertical only, and am going to build the next one horizontal only.
Then I'm going to build a cabaret for mostly vector games.
ALL of these will be able to use pretty much any controller that I have.
With regard to your design, I would watch the wrist rest distances.
Most people need about 6" from button center to comfortably rest their hands.
Joysticks will vary depending on grip style.
An over-the-top gripper will need about 4", a side-shaft gripper will need a bit more.
Make sure that you have sufficient distance between your trackballs, and the monitor bezel.
Smashing your fingers into the monitor bezel is only slightly more fun than smashing them into a joystick.
Also, I assume you are planning to cut the front corners off the bottom tier?
If not you better tell your friends to bring their cups if they want to play racing games.
If having it all is your goal, some things that you'll be missing out on with this setup are:
2-P Tank games
270 driving games
Yoke games
Analog stick games
All the SNK-type rotary games
Asteroids type games
(the current button placement doesn't make for easy 5-button gaming, especially for 2-P Space Duel)
Positional gun games
Whether this is worth it, or not, is a decision you have to make yourself.
Those of us that went modular weren't willing to trade current/future expandability for ease of use.
Those who chose smaller CP's, or frankenpanels, were willing to make that tradeoff.
Other considerations for me personally were that I also didn't like playing a 1-P game way over to the side of the cab, and hated trying to explain the controls to people.