Do you have the IH CNC kit? If you grab a hold of the pulley on the end of the ballscrew can you move push/pull it in and out even just a little? I wonder if you got the spacers that slip onto the ball screw turned around... you know... put the little one were the larger one should be and vice-versus. Or, perhaps the bolts on y-axis that hold the retainer on... you know the bolts with the bevel washers, are not tight enough (just a little goes a long ways). There were spacers that were included in the kit that I received that went under the retainer... did you receive/use those?
Just some ideas... hope they are along the right path.