I made this to align my x axis against the Y rods since this appears to be the best way to reference from. Tramming into the z axis tops leaves room for small differences due to extrusion length.
Images above show how the tool is placed. With power on Y forward and move Z to allow placement of the tool. Then power off and move the Z screws together to level out X to the top of the tool. Don't apply too much force.
Then power on, lift Z using the control panel and remove the tool.
I'm going to make a more rigid version of this tool, but it will take longer to print.
Print with in the longest side along the X axis. Seems like the best option, but just a suggestion. PLA is more rigid than PETG so I'm suggesting PLA.