what do you have your first layer height and extrusion set to?
the only reason the knob would be too large at the base is extrusion is too much, or you are smushing your first layer to the point where it is enlarging the print.
so i would try to do first layer height at 100% and extrusion at 90% for pla or 100% for ABS and see what happens.
the layer issues you are seeing (the fact that they arent in line) could be a number of factors, but most likely slop somewhere in the system.
I had those issues as well. now im getting prints that look like this. after only a few test prints.

First pic is before i had all my stuff slop free


this is after i tightened and tuned everything. stick with it.


picture doesnt do it justice.