Calibrating 12OClock before going through parameter optimisation is the intended way.
Optimisation does not correct 12OClock afterward.
I did not evaluate the effect of slack in the gearbox. Before reading the level, I would recommend preloading slightly with your finger in direction of the sled pull to see if it makes a difference, and how much it does. If you do, please repport about it
I invite you to review the error plots to help your evaluation:
