Wires - colours don’t really matter.
Plug your stepper directly into the board - If you plug the stepper in the wrong way round it will go the wrong direction. No problem, switch off, flip the plug and it’ll go the other way.
Extensions just need to be straight through.
Occasionally the motors can come with crossover wires - you can tell because the motor will just shudder not move. If that’s the case you carefully release the terminals from the plug using a pin and swap them.
Here’s a diagram of that
With the motor unpowered and unconnected to anything else if you short 2 pins together and get resistance when you turn the shaft - those 2 are on the same coil.
I can’t remember for sure but I would make the same assumption as you about the Y motor order. When I built mine I connected all the steppers to the board directly on the bench to ‘prove’ them, worth doing before starting to assemble imo.