The Ben Ish Hai (Rav Yosef Haim of Baghdad, 1833-1909) writes that after one recites the words, "Yoser Or U’boreh Hoshech" in the morning prayer service, he should take hold of his Tefillin Shel Yad and then kiss his hand. It is incorrect, the Ben Ish Hai adds, to touch one’s Tefillin Shel Rosh at this point, or at any other time during the recitation of the Beracha of "Yoser Or." There are those who do touch the Tefillin Shel Rosh at this point, and the Ben Ish Hai strongly opposes this practice. He notes that according to Kabbalistic teaching, there is no basis or rationale for touching the Tefillin Shel Rosh during the section of "Yoser Or." Of course, it is customary to touch both the Tefillin Shel Yad and the Tefillin Shel Rosh during the recitation of Shema, as one recites the verses that speak of Tefillin. During "Yoser Or," however, one should not touch the Tefillin Shel Rosh. This applies as well to the recitation of "Kadosh Kadosh Kadosh," when it is proper to touch the Tefillin Shel Yad, but not the Tefillin Shel Rosh.
There is a debate among the Halachic authorities concerning the proper way to recite the phrase, "Be’safa Berura U’bi’n’ima…" in the Beracha of "Yoser Or." Specifically, the debate surrounds the proper punctuation of this phrase. According to the scholars of Kabbalah, one should recite this phrase as follows: "Be’safa Berura U’bi’n’ima, Kedusha Kulam Ke’ehad Onim." This means that the heavenly angels sing "in a clear language, and with a pleasant voice; they all recite Kedusha in unison." According to this punctuation, one pauses in between the words "U’bi’n’ima" and "Kedusha," since "Kedusha" begins the next phrase. This is the view accepted by the Ben Ish Hai.
By contrast, the Abudarham (Rav David Abudarham of Seville, 14th century) punctuated this phrase as follows: "Be’safa Berura U’bi’n’ima Kedusha, Kulam Ke’ehad Onim." Meaning, the angels sing "in a clear language and with a sacred, pleasant voice; they all recite in unison…" According to the Abudarham, the word "Kedusha" is included as part of the first clause – "U’bi’n’ima Kedusha."
As for the final Halacha, both practices are acceptable, provided that one understands the text he recites and has the proper concentration as he recites the prayer.
Summary: One should touch his Tefillin Shel Yad – but not the Tefillin Shel Rosh – after reciting the words, "Yoser Or U’boreh Hoshech" in the beginning of the Beracha of "Yoser Or." There are divergent customs regarding the recitation of the phrase, "Be’safa Berura U’bi’n’ima Kedusha Kulam Ke’ehad Onim," as some make a slight pause after the word "U’bi’n’ima," while others make the pause after the word "Kedusha." Both practices are acceptable.
