Prusa calculator shows me 160 steps for X and Y and 5120 for Z. The dimensions of the square are 49.9mm along X axis and 47.5 along Y axis (2.5mm of difference). The “vertical” gap between the two edges of the circle is about 2.5 mm again.
The pen mount makes me immediately suspicious, it seems to me steady but tomorrow I will triple check it. I’m more concerned about the bars of the gantry: perhaps my 3d printings are not accurate enough? Or loosing all the nuts and then titghtening again could resolve my problems?