The Si software was updated to program the C board aux output via the network while using a single stage down conversion with a B board, and an A board to scan the power (block diagram in this post is still valid, but with A and B on one BBB and C on a separate BBB). The last cavity filter constructed was then scanned to produce the figure below. The vertical scale is in dB (but to convert to an absolute dBm takes some calibration and calculations that I haven't incorporated into the software yet).
This response was then compared to the filter response taken manually using a spectrum analyzer. That comparison is below.