If it completes the home cycle without any alarms, then basically you are fine. With the display on the position screen that shows distance to go, home the axis and read the dist to go. Rule of thumb is it should be around .120".
If it is way off and it bothers you, adjust the grid offset parameter for that axis until it results in the .120" @ dist to go after homing.
Don't forget to reset Y-axis offsets again when done.