Dimensions are all out of whack!

[Toddwagner]

So I've been working on getting my printer to print flat on the whole bed, and finally accomplished that. Today I printed two 50x50x50mm cubes and measured them and averaged the measurements... In the X-axis I was .25mm over, on the Y-axis I was .53mm over and on the Z-axis I was 1.17mm over. Not sure what could cause such a difference in the accuracies?
Edit: I do know to adjust rod length to get x and y to be bigger/smaller, but what do I do when they're off by different amounts? What about the z axis?