@corlissmedia Yes, I am suggesting to move whatever is in the middle of the endstop to the outer currently unused connector on the endstop. Not only does "normally closed" make them less susceptible to noise, you will also find issues with the wiring more easily.
since an endstop is just a button, it doesn't matter if green goes to one side and white to the other or the other way round. Either way you are connecting Ground and Signal. This is true for both endstop and control board side. Just make sure not to connect to the voltage pins.
I recommend you have a print out of the wiring diagram at hand. I would suggest using IO 5 and 6 for X and Y, using the in and gnd pins (your 3 position plug photos above indicate you did this). For Z you will need to use one of the 5 position IOs, I recommend IO4 (or any but IO0 and IO1 because those have special features you may want to use at a later time).