If one has a Shel Yad of Rashi and Shel Rosh of Rabbeinu Tam, or vice versa, may he wear them together?

Yes.[1] Some Poskim[2] rule he is to first wear the Rashi Tefillin with a blessing [whether they are Shel Yad or Shel Rosh] and only then wear the Rabbeinu Tam Tefillin. Others[3] rule one is always to wear the hand Tefillin first, although the blessing is only recited on the Rashi Tefillin.

[1] Shvus Yaakov 1:2; M”B 34:5; Kaf Hachaim 26:2

[2] Shvus Yaakov 1:2; M”B 34:5

[3] Kaf Hachaim 26:2