Take the measurements, calculate the average (by design 100mm) and change your steps in the printer firmware config with the following formula.

for X and Y: 100 x [step value] / [average measurements] = new step value
for Z use: 20 x [step value] / [average measurements] = new step value

Save your changed config and update your firmware. Instructions to that may vary depending on what printer you have.

On some printers you can adjust the steps or dimensional calibration directly in the menu.

Now reprint the Rig and measure again and adjust values if needed.

To see if your X and Y are physically rectangular to each other, take the 2 diagonal measurements average and compare them. if they are near equal to each other your X and X is alligned perfectly. If one is bigger than the other, you need to adjust the angle on your X or Y axis. To evaluate any errors also take a 90° angle gauge.

Reprint the model once again, take measurements and adjust if needed. Repeat the process until all the measurements are perfect.