LED and Photodiode Data Acquirement System
Hint 1: Do some experimentation to figure out if you really need all those complicated circuits. 


  we get bonus points if the system can detect what material the ball on the pendulum is made out of, ... was hoping for a hint ... .


Hint 2: You have three LEDs to work with, with different colors. Exactly how these might be used to detect the material of the ball depends a lot on the range of materials of the balls that might be used.


  Maybe a green one would be easier to detect since its light carries more energy?


Green light has more energy per photon. If you use IR, you can just send more photons to get the same intensity as you're getting from the green source. 

Also remember, the photodiode generally generates one photoelectron per absorbed photon. So the responsivity of the photodiode (in A/W) is generally higher at longer wavelengths, specifically because the photon energy is lower.