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Awesome!  I have everything figured out.

So, for the  histogram total pixel issue, all I have to do is make sure I uncache  the histogram.  Photoshop tells you when you need to with an exclamation  point in the corner.  If you don't, it may mess up the new histogram.  I  randomly figured this out from reading on a random forum.

As for the Record Measurements tool, I don't think  that is in normal photoshop BUT the histogram pixels is the same  number.  I confirmed this by using CS5 Extended at work and both  histogram pixels and Record Measurement area are the same values.  This  is even better news for me because it confirms that the hsitogram value  IS the area of the selection.   This allows me to use my conversion to  micrometers using the barscale on the image PERFECTLY.

Thanks for all your help!