mirror backplot

I've had this CNC with a closed-loop DC servo for a long time, and it works well for both movement and backplot with the home dot at x0 y0 as seen in the photo. The only problem is that it only works well with the y-axis inverted; the y-axis moves away in a negative direction. I decided to set the axis to positive as the x-axis, but the home dot moves to the left, and I haven't found a way to set them in step... basically, the plot moves outside the work area. Could it be that I changed the order of the pwmgens to match x and spindle on a 7i40hv and y and z on another to use two different voltages for the motors?