Before diving into spectral data configuration and FFT frequency resolution which I probably don't understand anyway, let me key in on a very important statement in your request, "even with a shaft fault existing such as misalignment or unbalance, the machine can live for years". This leads me to believe a simple PM to replace the bearing every 2 years may be preferred to trying to define a questionable low speed vibration monitoring system? Also, what is the COF (Consequence of Failure)? If this is a mixer or agitator that can be easily shut down for repair or especially if it's redundant, it may be more cost effective to run to failure or install one of the old "earthquake switch" devices on it to indicate a problem. Bottom line what's the ROI? Always invest your money and time in the best return.