MK3.9 Z-Axis Possible Solution
What worked for me:
Loosen the 4 screws holding each threaded Z axis motor/threaded rods in place and then lightly tighten them back. A total of 8 screws.
I have also had the same problem many of you have had with the Z-axis calibration. The nozzle wouldn't get near the print bed and then rise to the top and I would get the red X in the self test. I followed all of the recommendations given by Prusa in the troubleshooting section and the problem persisted. When I noticed that other people were having the same problem, the Z-axis not getting close to the print bed, I theorized that it's friction in the Z-axis. This was because it was stopping at various different heights.
At first I wanted to just lubricate the rods but I also thought it might be misalignment in the threaded rods causing excessive friction when nearing the build plate. So I loosened and then re-tightened the screws for each Z-axis motor.
Let me know if this works for anyone else!