Don’t mess with gcode until you have all the axis driving the right direction. There’s no reason to think playing a gcode file will fix things when a manual move is broken.
Are you sure you successfully flashed it? Send an M119 and see that there are X2 and Y2 in the report.
You might want to unset the digipot current, and change the driver type, but those changes would be subtle. Be sure to adjust the driver current with the little trim pot.
You can, I think it is in the advanced and it is something about “INVERT_Z_AXIS” or something.