I think Y is the more important now to address here! X and Z are easy to notice but if your Y is off you'll get some the parallelogram effect on the bed. And its more difficult to notice!
Ya, i didn't cover Y all that much I guess.. though the image "X toY" shows how to check it I may do one more little graphic image and add it for Y
helloyou can also have big trouble if your Y axis is not parallelbecause your bed will go up and down when y axis will move from side to side !!!
Here's your solution for the xLy orthogonality http://www.thingiverse.com/thing:1706669 I made this as I noticed right off my x an y were out of square and this did the trick truing them up. :)