Are the jacks going to connect to the pcb via wires? If so you can save pcb space by replacing the current jack part with 2 pin headers (which take much less space.) If they are mounted on the pcb I can’t see how that will work mechanically, the jacks will be parallel to the surface. The bottom row could work, but the two in the middle of the panel will not. This is something that you need to plan out before finalizing the layout of the parts on the board, you need to know how you are going to make it work mechanically before you cut (or even layout) the board. I’d actually suggest that you build the enclosure before you do the final pcb layout, so you know what the pcb needs to look like mechanically before you lay out the board. As I looked at your latest drawing, I saw we have both missed a couple of things. The mega will presumably be powered via a wall wart connected to the coax power jack (aka vin). The mega will then provide 5V for the optocoupler and the circuitry (but at present neither +5V nor ground are connected on the mega). Now there needs to be a different 5V supply (with much higher current than the mega can provide I expect) that supplies the two neo pixels. There isn’t a generic 5V power supply available in core parts (although there probably is one on the web somewhere) so in the modified sketch below I deleted one 1000uf Capacitor (as you only need one of perhaps higher capacitance for both neo pixels) and used a dangling wire in breadboard to indicate the neo pixel power source (that needs to be replaced with whatever will power the neo pixels). You also need to consider that power supply in the mechanical design for the case. You probably want to use numbers (as I have in this sketch, for me your Chewie original circuit.fzz above is saved as Chewie original circuit2.fzz to differentiate it from the previous versions with the same name and thus this new one is Chewie original circuit3.fzz. That way you can keep copies of earlier sketches to go back to when you make a mistake. In any case here is a new version of your last sketch with the power wiring changed in a fairly ugly manner :-).
Chewie original circuit3.fzz (128.5 KB)
Peter