How to define scan area?

The current state of the master build gives a range of motion that measures 11.8×11.8mm, and is square. I have been trying to work out how to determine the centre position reliably enough to know whether we should allow extra motion up on the actuator, or down (or both) to allow the full design motion of 12×12mm.

You will need basically all the parts new from the current master build. It is not just the main body that changed, the feet as well, and the sample clips.