I have finally worked through some of my issues with my cnc build. I have the A axis slaved to my Y axis with the limit proximity sensors on the back of the machine. When homing the Y axis makes it to the sensor before the A axis.
The company says they use it so the machine is always square but I can not get the 2 axis to be parallel.
I measured the sensors to make sure they are both identical length from the nut.