Mark, I view the first plot as a meaningless measurement, not ambient noise....
As it turns out, my ambient noise plot really isn't that bad. I certainly wouldn't recommend someone using a transfer function instead of a spectrum plot, but since my reference trace was in this case esentially random electronic digitl console noise, the transfer fuctions magnitude plot itself isn't that far from a single channel spectrum plot.
The trick here is that my refernce trace was essentially white.
Below is a comparison of using atransfer function versus a spectrum plot for measuring the ambient noise in my garage. The major events, like the fan noise at 56Hz, are basically the same on both plots.
One can try this experiment at home.
Again, I don't recomend using the transfer function to measure what should be a single channel spectrum measurement, but if your reference trace is low level white-ish noise the results won't be too far off, the math works fine.
Anyway, back on track, anyone have a comment on the system alignment?