Tonight we printed out the PCB pattern to scale, and tested how it fit in the case. Surprisingly accurate alignment considering that I can't focus on close up items any longer. However, we did realize that we forgot about the front post. So we will likely have to move some components to the underside of the PCB.
Here is the paper version taped onto the original board with the holes aligned and the directional js buttons laying on top of design. The components at the top center will need to be moved, as well as the diodes next to the existing fire buttons.