Photodiode connection to ADC
I guess it would be redundant to suggest that you should have breadboarded this portion of the circuit if you couldn't predict the current from the PD specs. That's a relatively small very fast PIN photodiode. 

I would suggest you replace the photodiode with either a much larger one or a phototransistor. There are phototransistors available in a two-lead package. 

Using such a high value resistor can cause issues with leakage and other factors (often there is a very significant loading depending on reading rate for typical MCU ADCs) so you would need to study the datasheet for whatever MCU you are using and maybe do some testing.