Today there were further modifications made to the ISS box in an attempt to get more suppression.
Modifications:
I attached the updated schematic, but several resistor values were changed in the filter stages. Additionally, we found that there were additional components between the PD input and the second page of the schematic causing problems, which are not pictured on the schematic. The link to the schematic for what goes on right after the PD input is here: PD input schematic. These additional components include an amplifier which was saturating our DC signal before it could get to the high pass filter. We removed the amplifier.
Transfer function and RIN:
The transfer function of the box plotted with that calculated in LISO is:

Unfortunately, problems arose in implementing the ISS with the above transfer function. The following plot shows the resulting RIN suppression, or lack there of:
Using the flip sign stage in the ISS box, the transfer function becomes:

Where there is clearly positive feedback in the phase. However with this orientation, there is a clear suppression of the RIN:

The corresponding frequency noise suppression is:

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