Psychopete:
One thing that came to mind is if I use an op-amp, would that essentially kill any voltage left for the ADC to read?
I guess that depends on the input impedance of the op amp you use. Since they tend to be high impedance, I'm not sure what the overall effect would be.
If the goal is to just increase the signal's voltage in order to pass the high threshold of the digital inputs, is an op-amp necessary? Couldn't you just use a simpler transistor?