If you are going to use the happs 3" mount plate, it is 6.5" square, the same as the height of your CP. Which would mean you'd need to center the TB vertically.
FWIW, you can overlap some of the button's "skirt" over the TB mounting plate if you counter sink the plate level to the rest of the CP (I've done this). The button holes should be outside the mounting plate, unless you plan to drill through the edge of the plate.
I'm pretty sure you can mount the joystick partially underlapping the TB mounting plate, too, but I haven't tried this.
Of couse, if you aren't going to use the mounting plate, then you can ignore everything above.

For trackball games, you only need 3 buttons (missle command), but spinner games and joystick games you plan to play may need four. I agree that six vertical is too crowded.
EDIT:
you posted the new edition just as I was going to post this, so instead of edditing the above, I'll just add below.

I like this new layout better, but remember the 6.5" mounting plate.
You might want to arch your buttons instead of slanting left, so it won't feel funny when playing trackball games, plus missle command had the buttons arched.