Per Sieg the maximum acceptable runout at the end of spindle 0.0008"/0.02mm and 2"/50mm below the spindle is 0.0016"/0.04mm.
The runout 2" below the spindle is difficult to accurately measure because the runout of the toolholding system and the tool itself needs to be taken into account. Instead, to check the parallelness of the spindle bore to the spindle axis I think it's easier to measure the runout just inside the bore and then again an inch up inside the bore. If the bore is parallel to the axis then the runout will be the same.
Having the spindle not be exactly concentric with the spindle axis is almost unavoidable in these machines since the bore is not ground with the spindle already mounted. This is why it's important to correctly stack your tolerances: http://benchtopmachineshop.blogspot.com/2015/04/mill-stacking-tolerances.html.