I hope I'm not too late to answer this. I just discovered this website.
The Ember printers were calibrated digitally, but this calibration was for the projector relative to the base. The tolerances on your specific resin tray, vat support plate, and window will all affect how accurate your assembled printer truly is.
To calibrate the projector you will need to disassemble your Ember once to loosen the screw holding your projector in place. It is just to the left of the projector lens and should be pinching down in a slot on the projector housing. Once this is loose, you can calibrate your projector with a 2.5mm hex wrench on the long bolt located below the back of your projector. Also great is that this bolt is accessible while the printer is assembled so you can modify the calibration on the fly.
As for calibrating to perfection, your best bet is to calibrate with paper from the window of your specific resin tray (clean of course). If you'd like to build a contraption that detects the showcal image line at exactly 64 and 40 mm you can, but a drawn rectangle on paper can get you pretty darn close. The best thing to do once you calibrate the focus is to print and measure. The amount of light getting through the projector lenses and PDMS window can vary from printer to printer, not to mention your material and print settings will have a large effect as well. So of course use the tray, material, and settings you prefer and then measure the produced print in relation to the digital dimensions and alter your image scaling from this.
I've done high tolerance stacked prints on Ember and we used this procedure to get extremely accurate parts.
Let me know if I didn't explain anything well or if you have any questions.