also sounds as if you have some binding in the ballscrews or slides , refering to your point of bump bump every 2 revs , try removing the steppers and turning them by hand
to feel for any roughness binding or stiffness first, both on your slides and screws , make sure your sliding surfaces are clean and greased too .
if all the motors are the same type , then the same settings should get you near or at least into the ballpark and then fine tune from there