What I did to check perpendicularity on my mill was to clamp a good known 8" engineers square to the table and mount a lever arm dti in the spindle. I then adjusted the square to achieve 0 deviation on the x traverse, rotated the spindle 90° and measured the y deviation by traversing the other leg of the square. In your case you could use the x & y reference edges to do something similar. A set of good parallels would allow you to check y alignment at various x positions. Obviously you don't have a spindle yet so you'll have to synthesize some sort of temporary and fairly rigid fixed height z axis.