Since your CP is only 18" wide, I would do the following: move the spinner and trackball in the middle and put the buttons on the right. And if you plan on playing any Neo-Geo games, you should rotate your buttons layout 90 degrees counter-clockwise. Then the top row of buttons would loosely fit the buttons pattern of the 3rd revision of MVS cabs.
I know the buttons will then seem to be too far apart, but that's on paper and you should try to do at least a cardboard prototype before dismissing an idea. IMHO the distance between the joystick and the buttons would be more comfortable than your proposed current layout.