There was only one flying 747 prototype......The City of Everett, which belongs now to a Seattle museum.
The 2nd 747, N747PA, was broken up last year.
The third was a static test frame that never flew.
As with the 777, flight testing was done by a variety of actual production model 747s before delivery to Pan Am.
I believe NASA uses a couple of -100 models to carry the Space Shuttle....plus they fly an -SP in their SOFIA project....could that be the one you're thinking? What number -SP off the line is being used in SOFIA.