So it relocates the main rotor to the far right (instead of the middle) and I believe that is why everything has been thrown off. Everything else about the laser remains the same and yes it worked previously.
Start the machine with the laser head in the middle of the frame. Using jog controls does the laser move as expected? Left goes left, right goes right, up goes up, down goes down?
If not, make sure you haven’t connected the cable to the X-motor backwards. Also, did the kit come with an updated cable? It’s possible that the direction of the motor has been inverted but I can’t imagine Sculpfun doing that without a hardware solution or instructions to change this.
I suggest you revisit this. You almost certainly have swapped the X and Y cables or plugged them into the wrong port on the controller. That likely is the cause of your issues.