I levelled the coin 'A' letter scan with a spreadsheet. The upshot is that as the Y movement goes positive, the Z position goes positive by 0.06 times the Y movement. When the X movement goes positive the Z height goes negative by 0.02 times the X movement. These effects are cumulative. Correcting this with the spreadsheet gives the following scan:
This can obviously be corrected preferably in the firmware but for the moment I intend to write something to pre-distort the gcode. But now I know by how much!
The dark purple patch in the top right is a visible contaminant on the coin that required additional force to either move or penetrate and so shows as a deeper contact point. If we correct this, and flip the X axis to correct the fact it is inverted, we get:
There is now a visible defect in the crossbar of the 'A', and indeed if we look closely at a micrograph we can see it:
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