James did you check how many teeth are on the Y-axis motor pulley? The mach3 wizard has got you very close, but diagnosing the problem properly by counting the pulley teeth is better as that gets it spot on. Also this means the Z-axis is also out by 7% if you've not already changed it. If it's 28T on the Y and Z motors and 30T on the ballscrews put 85.71429 (i.e. 400/5*30/28=85.71429) in the motor tuning for both.