Here is my procedure for getting the X perpendicular to the Y axis on prusa style printers. (assuming system is built and bed is level)
Best practices when assembling. Locate as precise as you can the frame (my Z axis uprights were off 3 mm)
tape a piece of graph paper to bed (machine is off)
fix a mechanical pencil to the printer head (tooth pick can work) position so the lead is close to the paper or just touching.
move printer bed y axis to front of machine, move x axis to about the middle of the x axis and just over one of the lines on the graph paper.
move y axis to back, is pencil lead aligned with line on graph paper? No? adjust graph paper, repeat until pencil aligns with the graph paper the full travel.
6 move y axis approx to middle of travel and end of x axis stroke, line up pencil with perpendicular line on graph paper.
- move print head to the opposite end on the x axis. does pencil lead line up? no make adjustment to uprights and repeat until runs true.
This is my first has of this. let me know what you think.