Any link to that?
Usually there are two very different measurement modes:
A) Testing (new) machine, bit like 16.4.9. (a) Column ways of knee square with table et.al.
http://what-when-how.com/metrology/alignment-tests-on-milling-machine-metrology/B) WHEN REBUILDING - you need to find first primary reference and then work from there.
I.E. you have very limited means to spindle axis you need firts to check that spindle is fine, no use to measure from the spindle if it droops 0,1 mm down due to shot bearings. When you are positive that spindle is fine, you can hook an arm to it and have a dial indicator from it. If the column is pretty close to upright (dial indicator reading is not efffected gravity bending the arm) then you can have readings on that swing arc - that will establish that those two points are in a line that should be pretty damn near perpenticular to spindle axiss.
You need to find two points near spindle and two from bottom - secret is to use area the is not worn, then assume that it was originally right, establish a plane and measure how much worn areas differ from that plane. It's way too easy to make something straigh, even planar while it is grossly skewed from the original plane. Important step is to avoid it from the start. You establish the plane and you need to down with that plane and ressist temptation of just making a flat surface on any random plane.
I think it is best first to check the upright column to spindle axiss and then knee to column/spindle and last the table.
It is fine to measure table and all the to spindle, but that just tells how much it is off from ideal with that load whatever you have on the table. Very little where the error is.
Is this any use (it is somewhat CNC stff, but carcass is manual machine):
http://www.practicalmachinist.com/vb/general/small-mill-reconditioning-conversion-234739/Pekka