What material are you cutting there? How many flutes on the endmill? 2-flute carbide from us? Have you considered single flute HSS?
We have sample files for tramming a wasteboard at: Wasteboard Plans with threads — We have a bit about tramming on the wiki: https://www.shapeoko.com/wiki/index.php/Calibration_and_Squaring_the_Machine#Tramming