Just a quick noted about some resudual beam spots I noticed after the second PBS in the south path (after the AEOM).  

When I went to minimise transmitted power through the second PBS with a power meter two spots were present and most obvious. I didn't really understand where these would come from.  Checking further up the path, these features are not present before the AEOM and PBS. I swapped out the PBS, then the waveplates: no change.  I then compleatly removed the AEOM from the path (but not the PBS) and the spots were removed. The beam looked well centered (by eye) and had good cleanance from the edges of the aperature.

Antonio thought it might be some alignment issues with the modulator and did some precition alignment.  His method was to look at power at the output and maximise (we measured power of 296 mW and out of 280.7 mW which gave an loss of ~5%).  He also fixed the CCD viewer position and compaired the computed center of the beam with the AEOM removed and then installed. This seemed to improve the non-polarisation filtered beam throughput and improve the shape of the beam.  

The optimal operating point for the AEOM should be at 50% throughput through the PBS so the remianing junk spots should be small. Still not sure what effect is producing the residual remaining spots were. This is something we should keep in mind.