Glad it's solved! Easy. 
For next time / next reader: on those connectors, with a small screwdriver or the end of a knife you can actually pull the little plastic tab up and pull out the individual metal pins... To change the motor direction you only need to swap one coil pair (although flipping the whole connector does the same thing!).
Would have saved grinding the connector back hehe.
Note also the motor direction can be reversed in firmware, but the physical method is usually much much easier!
SD3. Mk2b + glass, heated enclosure, GT2 belts, direct drive y shaft, linear bearings, bowden-feed E3D v5 w/ 0.9° stepper
Smoothieboard via Octoprint on RPi