I ended up taking the absolute value of each signal, then using the Pythagorean theorem with those absolute values, and then multiplying by the sign of the average of the in phase and out of phase. This worked relatively well, and definitely works for the amplitudes. However, it doesn't quite...
To skip the background of my question go to the last two lines of this post.
I work in a materials science lab doing spectroscopy with a rather crude type of instrumentation. We use modulation to improve our signal to noise ratio, and we record two signals, one in phase, and one ninety...
