I feel the pain here, I use Degenatrons plans for scratch builds and Jstik/button placement drives me out of my mind.
Your gonna have to modify your plans to lengthen the height of the CP to push the Jstiks further up to accomodate those buttons, most folks use the standard long barrell buttons.
I started putting buttons on the sides.
I would think 80mm should be big enough to support any jstik and still give you room for your buttons.
Oh yeah, gonna get me that nintendo looking genius contraption you done went off and designed