Try using the new beta firmware, with your correct z axis steps, It has slower z axis accelerations. That should help. It could also be binding of you axis so check to make sure it moves smoothly and very easily by hand for the whole travel.
There are a lot of reasons your bearings might not touch. Sometimes it just doesn’t matter, but if it is causing issues I would double check your center assembly for square.
Reply To: MPCNC Printer Setup Problem