I don't have a good explanation why, but I too measured similar numbers to what Koji measured. The overall conversion gain for this board (including the +20dB gain from the daughter board) was measured to be ~5.3 V/V on the bench, and ~16000 cts/V in the CDS system (100Hz offset from the LO frequency). It would appear that the effective JMS-1-H conversion loss is <2dB. Seems fishy, but I can't find anything else obviously wrong with the circuit (e.g. a pre-amp for the RF signal that I missed, there is none).

I also attach the result of the measured noise at the outputs of the daughter board (i.e. what is digitized by the ADC), see Attachment #2. Apart from the usual forest of lines of unknown origin, there is still a significant excess above the voltage noise of the OP27, which is expected to be the dominant noise source in this configuration. Neverthelesss, considering that we have only 40dB of whitening gain, it is not expected that we see this noise directly in the digitized signal (above the ADC noise of ~1uV/rtHz). Note that the measured noise today, particularly for the Q channel,  is significantly lower than before the changes were made.