To transfer data from the Yokogawa SA2400, the only way is through the GPIB port. (otherwise, there is an oldfashioned paper plotter)
So, I wrote a labview program to read the spectra and save it on a file, based on a library I found here: http://sine.ni.com/apps/utf8/niid_web_display.download_page?p_id_guid=E3B19B3E936A659CE034080020E74861   
The list of commands for the GPIB is in the  (in Japanese sory...) manual I uploaded to the wiki: http://gwpo.nao.ac.jp:8989/wiki/Documents?action=AttachFile&do=view&target=SA2400+GP-IB+manual.pdf
I did some spectrum acquisitions of the photodiode signal. Average number 64. in several conditions.

Plot 1. spectrum in dbV (not normalized per rtHz)

20180625-unplugged               (noise without anything  connected)
20180625-unplugged400khz    
20180625-50ohm                     (noise with the 50ohm terminator
20180625-50ohm400khz          
20180625-darkT50ohm            (PD dark noise with a T and 50ohm terminator)
20180625-darkdirect                (PD dark noise 
20180625-darkAC                    (PD dark noise after the high pass filter box)
20180625-darkACT50ohm       (PD dark noise after the high pass filter box with a T and 50ohm terminator) 
20180625-darkDC                    (PD dark noise after the high pass filter box)

Plot 2.  spectrum in dbV/rtHz ( normalized per rtHz)
noise floor

Plot 3.  50ohm terminator as input of the SR560. Icreased the gain of the preamplifier to check where is the noise floor of the SR560.

Plot 4. Comparison of the noise floors of SR560 and PD dark noise

Plot 5. Laser on / off

to be compared with the noise on the HeNe PD