It has been years since I messed with this, but as I recall, and more memory will fade in later as I think about it, the goal is to measure the axle pinion angle and the transfer case pinion angle and they should add up to 180* with deflections in opposite directions. We did it using the yokes, a magnetic torpedo level and and angle finder on the level. Add (Or subtract, depending on which end or which way you are going) 90* from that measurement. The only way to fix these is tapered shims between the axle and leaf springs on the axle end of the shaft.
Been a long time, and my memory could be off, so maybe there's a better answer out there.
Ray