Index error, horizontal axis error and collimation error are regularly determined by calibration and are removed by mechanical adjustment.
3.
Any discrepancies between eye focus and measured focus which manifest them & shy; selves across a range of distances within a single lens may be collimation error with the lens, but if such discrepancies occur across several lenses, it is more likely to be the flange focal distance or the groundglass ( or both ) which are mis-set.