I’m not sure if I’m looking at this photo correctly or not.
If those are normal Molex connectors, please note that to me it looks like the JST plastic shields are still on in place.
Leaving the plastic shields in place, normally results in loose stepper motor connections.
The instructions state to remove the shields to avoid loose connections. Others have replaced the Molex with JST connectors.
I’m not completely sure I’m seeing this correctly or not, as with your troubleshooting to figure out the blue/green swap, you saw how nice and tight the JST connector was. And maybe might have noticed how loose the Molex was compared to the JST? If yours are nice and tight, or you’ve already pulled the shields, my apologies.
“Depending on what wires you are plugging in you can take them off the end stops and stepper ports. Even after doing this you should always constrain your wires directly after the connection to the board to prevent them from wiggling loose.”
I did put cables from JST-to-Dupont cables between the board and the cable that comes from the stepper. This photo was to demonstrate what was going on. If you look closely you can see the left one has 4 separate 1p headers, the right one is 1 4p header. Its a lot easier to test with 4 dupont headers than it is with a JST having to repin them constantly.