Coming from making my own joysticks/cabs w/ custom and non-custom layout, I just gotta say you need to give those buttons a semi-arcade feel. The big problem w/ custom layouts is the spacing, basically if you don't want your hand to hurt the next day after extensive playing, you gotta keep the buttons close together. Even if the natural length of your fingers are straight out, they keep the buttons close together because you naturally curl your hand like a fist. Imagine if you used a mouse that was made of a wood block. It might work at first, but give it 2 hours and carpotunnel would be inevitable.
Let me give you an example of my own findings -

This layout looks perfect for my fingers right? Wrong, this thing is a freakin pain to play on. It's actually sitting in the corner of my room because the layout was so far spaced, an hour of street fighter and my fingers are dying.

Now that's more like it, I kept the horizontal spacing of the buttons AS CLOSE AS POSSIBLE. The curve of the middle button feels good for my hand, but I kept the classic capcom control panel style. The thumb button is for my Neo Geo days (
www.klov.com if you want to see a neo geo cabinet w/ this layout, I think only japanese players and hardcore snk-neogeo freaks use the thumb button though ) but I've found its the best layout I could have done.
I've also done the traditional 3x2 layout, which although it LOOKs boring, it FEELs great.
Last note about control panel - MAKE SURE YOUR BOLTS ARE FLAT ON THE TOP! I only exclaim this because the screws on my current control panel don't have covers and they can get really irritating on your hands. Make sure you have flat bolts w/ washer-nuts screwed in from the bottom.
-Good luck, looks like a cool project so far.