The connector that’s plugged in there is the DF13 one, and the black GND wire is in pin 4 - the JST-GH connector is the one with the orange tape.
Looking again at your footprint diagram, either the pin numberings on that are the wrong way around, or you’re looking at it in the software from the bottom (‘through’ the board) instead of from the top. The wire side connectors have a marking for pin 1, and they would both be on the far side of your latest photo, where the DF13 red wire is plugged in 
If your pin numberings are in fact the wrong way around on your footprint then you’ve correctly corrected for that in your suggested numberings for the signals, but I would advise against using that in a design because it doesn’t follow the manufacturer’s connector specification (the official pin 1 would be your pin 4). That would still function fine, but is unnecessarily confusing, and could be problematic later when debugging.