The Ben Ish Hai (Rabbi Yosef Haim of Baghdad, 1833-1909), in Parashat Vaera (5; listen to audio for precise citation), discusses a number of different Halachot relevant to the Torah obligation of reciting Shema. He codifies the requirement to recite the morning Shema before a quarter of the day (or the end of three hours as defined by Halacha), and emphasizes that in the wintertime, when the days are short, the time-frame for reciting Shema is also quite short. One must therefore be very careful – particularly in the summer – to recite Shema before the proper time, as otherwise he does not fulfill the Torah obligation of Shema. On Shabbat, especially, when the morning prayer services usually begin later than on weekdays, special attention is needed to ensure that Shema is recited before the final time.
One cannot "make up" a missed recitation of Shema. If one did not recite Shema before the final time, he can no longer fulfill the obligation. He can certainly read the Shema and will be rewarded for reading verses from the Torah, but he cannot fulfill the Misva of Shema.
The Ben Ish Hai writes that before a person begins reciting Shema, he must have in mind that he fulfills the Torah obligation of Shema, as well as the Torah obligation to affirm the belief in the oneness of the Almighty ("Yihud Hashem"). One should cover his eyes with his right hand before he begins Shema, and keep his eyes covered until after he recites, "Baruch Shem Kabod Malchuto Le’olam Va’ed."
Halacha requires concentrating on the meaning of the first verse of Shema ("Shema Yisrael Hashem Elokenu Hashem Ehad"). If one finished the verse of "Shema Yisrael" and then realized at that point that he had not concentrated on its meaning, he must repeat the verse. However, he should not repeat the verse immediately, as the Gemara forbids reciting Shema twice, which would give the impression that one acknowledges the existence of two deities, Heaven forbid. One should therefore pause before repeating the verse of "Shema Yisrael." The Ben Ish Hai rules that one should pause for the amount of time needed to recite the paragraph of "Ve’ahabta," which is approximately one minute. If one wishes, he can simply recite this paragraph to ascertain that the requisite period of time has passed.
The Ben Ish Hai rules that concentration while reciting the verse, "Baruch Shem Kebod Malchuto" is also indispensable for fulfilling the obligation of Shema. One who recited "Baruch Shem" without concentrating on its meaning must repeat it. In order to preserve the proper sequence, he should repeat "Shema Yisrael" and then proceed from there as usual.
Summary: One must ensure to recite the morning Shema before one-quarter of the day, as otherwise he does not fulfill the Torah obligation of Shema. One must concentrate while reciting the verses of "Shema Yisrael" and "Baruch Shem," for if he fails to concentrate on the meaning of either verse, he does not fulfill his obligation.
