Have you considered a positive feedback capacitor with the op-amp, to try to make an oscillator?<p>Then the illumination on your LED will affect the phase of the oscillator. By trying to make it oscillate at ~10Mhz, and then sampling the data, you should avoid the clipping problem, and you'd have a lot more data to use to potentially extract interesting things with clever math.<p>Even if the oscillator runs at 10Mhz, you don't have to sample at 10 Mhz - you could sample at a lower frequency (which must be clock cycle accurate) and make use of aliasing to still measure phase shifts very accurately.<p>You're totally going to measure the power supply, temperature, radio signals and a whole host of other things at the same time, but with the right signal processing/modulation you should be able to extract the effects you need.