This project shouldn't be too hard. I'd replace a lot of the analog circutry with a microcontroller with an AtoD converter. Debugging microcontrollers is much easier than debugging analog circuits for someone who is just getting started in electronics. So all you need is two photodiode or phototransistor amps (I like photodiodes because they are more linear) connected to two analog inputs on your microcontroller. The microcontroller can handle comparing the two values and generating the output.
Brent