I have heard an opinion that one should recite Birkot HaShachar (from LaSechvi Bina) at home before attending Minyan. However, most Siddurim hold that these Brachot be recited with the Tefillin on already. Which is the preferred practice- before or after putting on Tefillin?

One can recite all of Birkot Hashacher before putting on Tefillin . However it is better to do like the Rosh did, he recited the Brachot up until "Oter Yisrael Betifara" (not included) before putting on his Tefillin , than he put them on and continued on the rest of the Brachot starting with this Bracha. Rabbi Ya'akov Ariel