Reference Cavity Re-alignment
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The reference cavity transmission has steadily degraded over time from ~1.1V a month ago down to the ~0.4V when Jeff reported the problem to me.  A quick look at the alignment using only the periscope adjustments, did not make things any better and in fact I made it a little worse, leaving the transmission at ~0.22V (as displayed on the MEDM screen).  That indicated that either the alignment into the AOM was off or the RF level to the AOM was off.

Measured RF on oscilloscope, with 50 ohm input.
freq = 79.4 MHz
peak-to-peak amplitude = 21.66 V
Vrms = 7.965 V

So the RF level into the AOM is 1.27 W.  This is about the right level for maximum diffraction efficiency.  Note that the maximum RF power into the AOM is 1.3 W.

zero reading on power meter = 2.7 mW, power meter used is the Ophir thermal calorimeter
no measurements have been corrected unless otherwise noted
power incident on AOM, measured after PBS = 57 - 62 mW
power incident on 21.5 MHz EOM = 21 - 23 mW
this represents a double pass efficiency of ~ 22/59.5 = 37%
or a single pass diffraction efficiency of ~61% (Sqrt[37%])

After adjusting mostly the height of the AOM, the power before the 21.5 MHz EOM was 26 mW or 66% single pass diffraction
efficiency, further tweaks to the height resulted in 34 mW or a single pass diffraction efficiency of ~76%

Tweaked alignment into reference cavity using the periscope - mostly height adjustments; measured reference cavity transmission is ~710 mV on DMM, ~1.16V on MEDM display.  This is as good as the value from over a month ago.