a possible explanation for the lack of high homogeneity of our measured Jones matrices could be the not collimated enough beam.
I installed a f=-50mm lens as in figure 1.
I installed razor blades for beam characterization
when z = 25mm, blades are at 68 mm (last steering mirror to rotator mount) + 21 mm (rotator thickness) + 58 mm (rotator to blade) = 147mm
horizontal cut of the beam at (x,y,z) = 360,67,25
vertical cut at (x,y,z) = (315,140,25)
After going through the few lenses we have left, I found that placing a f=-50mm between the shutter and already installed lens f=50mm, I could get a somewhat collimated beam across few meters.
The lens is mounted in a removable magnetic mount for quick switch between absorption and birefringence measurement (fig 1).
Using razor blades, I obtained a beam size of about 900 um (in fig 2 which is showing both vertical and horizontal dimensions of the beam).