If I find a Rabeynu Tam Tefillin and I do not have another one, can I take it apart, and change the rosh (I know how to) from Rabeynu Tam to a Rashi Tefillin?
You are not allowed to. This is because the two opinions mutually invalidate one another and therefore you would be taking Kosher Tefillin and making it not Kosher according to Rabbeinu Tam. This is considered to be Mezalzel in the shita of Rabbeinu Tam. See the Ridvaz Chelek-6 Siman 2286.
This is Asur because it goes under the category "Maalim BikDusha WeLo Moridin." (Od Yosef Hai Wayera #8. see Oserot Yosef 3:6).