Rotary Scanning

Good day Forum
Have a question on point scanning and data file creation. I'd like to scan a part log the xyz coordinates, compare them based on simple math , then adjust the g-code trajectory based on the lowest value of the scan. any suggestion ?

Kindly
 

This might be as simple as setting the G54 (or similar) coordinate offset with a G10 command using the measured value.
Then leave the G-code unchanged, and based on G54 zero as the low point.