Photodiode temperature compensation
I don't see how subtracting one temperature-dependent signal from a smaller temperature-dependent signal does much of value. Perhaps you could explain, using equations rather than words, how you think this could work. 

The "known light source" is probably going to turn out to be more difficult that simply measuring and compensating for temperature directly. 1% for 10°C is not a very strong temperature dependency, so you should not need much accuracy in your temperature measurement/compensation circuit. 

The output of LEDs, for example, vary with temperature and time. Photodiodes are at least pretty much time invariant. 



Edit: I don't see anything wrong with this, but I might be missing some subtlety of PD behavior. Obviously it will depend on the photodiodes being matched in characteristics and at the same temperature. The dark current and shunt resistance compensations should track. 

I'm not sure what the point is of giving the dark reference PD any light at all. If you give it much light the bias voltages will remain matched but will change from almost exactly 5V to a bit less.