The gemarah says that to wear tefillin a person needs to have a clean body like Elisha baal kenafayim (shabbat 49a). How does the gemara know that Elisha had a clean body?
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I think you are misunderstanding the Gemara. You are taking it that we know that Tefillin require a Guf Naki from Elisha Baal Kenafaim. The point, however is different. It is that the Guf Naki has to be to the degree that Elisha Baal Kenafaim had one, to the point where he merited the miracle. It is an emphasis on how careful you have to be with it, not the source of the concept.
Tosfos answer, because a miracle occurred for the sake of his wearing tefillin. Only if he were wearing tefillin properly, i.e. with a clean body, would he merit such a miracle.