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Also, if you take into account that all components change their nominal value in temperature, so the fact that it depends on beta, and you resisitors and BJT changes in temperature it makes it floating. What I mean is that during normal funcitoning it will get hotter and that will change the output you calculated.
even though there are people who have this knowledge you are asking too much. Take a book from the library and read chapter 1 about charges. Many of these questions will be answered.
If I were you I would start by making the configuration with first and second input(your second and third paragraph). You only need gates and multiplexers. The third step is more interesting as you have to modify a little bit the alredy existing circuit.
Question. Do you turn off the source of sinuoidal signal after modifying the frequency? From your description I understand that in the begining you have 2 Sinusoidal signal in SYNC but one if shifted. What i try to say is that is seems that you lose SYNC of the input signals. Could you check it with scope. Also you could use INA128 instead of OPA2111 + INA105.