I noted the Z stepper misalignment before I even lifted the unit out of the crate.
I also noted that the misalignment of the various parts in the milling section contributed to the overall inability to tram the mill.
For example on my machine none of the holes in the 1/2" thick steel plates that the Z-axis ball screw thrust bearing flanges were attached to were consistent.
Note the difference in the preceding photos.
I also noted that the ballnut lead screws that lifted the milling assembly was not centered either in the top mounting plate or the moving carriage.
I was never able to tram the mill properly as if I made the tool face perfectly parallel with the milling table it would deviate in the X&Y Axis when traveling vertically.
If I made it not deviate in the X&Y direction during the vertical travel the tool face was no longer parallel.
I also noted that there was an increase in torque required to raise the mill as it got near the top end of the travel and I suspected it was due to the ball screw misalignment.
When I relaxed the six linear bearings by removing the entire top frame, having the milling carriage supported and removed the bottom bolts I measured the 6 vertical linear bearings for alignment using the same tools and techniques as used for ensuring motorcycle forks are aligned,
None of the 6 vertical linear bearings or two Ball Screws share a common axis and deviate randomly from true vertical with respect to the mill head carriage. Given that these are solid hardened steel shafts, this is an issue that cannot be adjusted out by having larger than normal holes in the upper and lower attachment points. As all you are doing is forcing the shaft and bearing assembly to accommodate the differences in x & y coordinates by bending to accommodate the deflection when traveling between the two extremes.
The two linear bearings on the tailstock end are out of true vertical with respect to the mill carriage by .35 mm and .44 mm, they are off by .6 mm with respect to each other over their full length.
The four linear bearings on the headstock end are out of true vertical with respect to the mill head carriage by .15 mm , 22mm, .18mm and .17 mm in random directions and with respect to each other the maximum deviation is .28 mm over their full length.
The two ball screws are out of true vertical .32 and .26 respectively over their full length.
It was useless to try and tram the mill until all these missalignments were corrected.
I initially tried scraping the paint off and it offered a slight improvement but eventually had to grind both the top and bottom of the milling carriage.
The top and bottom of the milling assembly was found to be not parallel.
Additionally the guide holes that the linear bearings and ball screw assemblies were to go it were not bored perpendicular and were actually at an angle.
Nor are the actual landing locations for the 6 linear bearings at the same Z datum on the headstock or by the tailstock.
Plus the attachment holes were crudely drilled and tapped adding to the misalignment issues.