Diagram of initial board drawing:
Meghan's amended drawing (with a few less background images, and my best attempt at explaining how the system works from current knowledge):
The reference and return photodiodes will convert the light signals they receive into current; from that current, we need information about what wavelengths of light were received. From searching basic information about photodiodes, they have a response parameter (speed/time) determined by the materials out of which they are made, which affects sensitivity in different wavelength regions. For example, PIN photodiodes are faster than P-N photodiodes.
This example PIN photodiode seems to be sensitive to IR and visible light, and has a parameter
$$ \frac{1}{2}$$
After speaking to Dr. Morin about the structure of Physics 90r, it seems that at the beginning, there is some form that the student fills out indicating they have spoken to their advisor about expectations, and at the conclusion of the semester Dr. Morin reaches out to that person for a grade. So, the agreement is entirely between the student and the PI.