^ 2.For a more extensive outline of the laws of Birkot HaTorah, see further in this book, 10:2 and note 2. Concerning Elokai Neshamah, the Mishnah Berurah 52:9 and Bei’ur Halachah write that the Pri Chadash maintains that one fulfills his obligation by reciting Birkat Mechayei hameitim. The Chayei Adam and Derech HaChaim quote him. However, Ma’amar Mordechai disagrees with him. That is also what the Pri Megadim understands from the Rama’s words, and what we can infer from the Gra’s writings. In any case, in order to avoid uncertainty, one who skips Birkot HaShachar in order to pray in a minyan should first recite Elokai Neshamah. If he did not recite it, he may not recite it after the prayer service, for safek berachot l’hakel, (when there is doubt regarding the recital of berachot we are lenient). However, the Bei’ur Halachah writes that one may rely on all of the poskim who maintain that one may recite Elokai Neshamah after the prayer service. Further, the Mishnah Berurah writes that if he explicitly has kavanah in Birkat Mechayei hameitim not to fulfill his obligation for saying Elokai Neshamah, he does not fulfill it and he may recite it after the prayer service. However, the Yechaveh Da’at 4:5, in the footnote, writes that this kavanah does not help. According to this, if, in the middle of saying Birkot Keriat Shema, he remembers that he did not recite Birkot HaShachar, he should recite Elokai Neshamah even between the berachot, so as not to miss out on saying it altogether (Yalkut Yosef 46:23-24).

^ 3.The Derech HaChaim, based on the Magen Avraham, writes that the laws of Birkot HaShachar are equal to the laws of the Amidah, and just as the time of the Amidah lasts four proportional hours, which is a third of the day, so does the time to recite Birkot HaShachar. There are those who maintain that just as b’dieved one may recite Shacharit until chatzot (halachic noon), the same is true for Birkot HaShachar (Rabbi Shlomo Kluger). Kaf HaChaim 71:4 writes that if one already prayed Shacharit he may recite Birkot HaShachar within the first four hours of the day, and if he did not yet pray Shacharit, he may recite them until chatzot. However, according to the majority of poskim, Birkot HaShachar are not directly linked to prayer, and one who forgets to recite them in the morning may recite them the entire day, and that is what is written in Mishnah Berurah 52:10 and Rav Pe’alim 2, Orach Chaim 8. (According to the Gra, if one forgot to recite them during the day, he may say them even at night until he goes to sleep. The Yalkut Yosef 46:25 writes that one who practices this way has on whom to rely.)

^ 4.Regarding the berachah, Hanoten lasechvi vinah, the Shulchan Aruch 47:13 writes, based on the Rosh and the Tur, that he must wait until the light of day begins to appear in order to recite it. The Mishnah Berurah 47:31 and Bei’ur Halachah write that the Acharonim (Magen Avraham in the name of the Zohar, Pri Chadash, and the Gra) agree that even this berachah may be recited before daylight arrives. However, the Chayei Adam writes that l'chatchilah if one recites it before daylight, he should be careful not to recite it before he actually hears a rooster crow. The Mishnah Berurah concludes that b’dieved one fulfills his obligation even if he recites it before hearing a rooster crow, as long as he recited it after chatzot. Kaf HaChaim 30 writes in the name of the Pri Chadash and the Chida that according to the halachah and the Zohar, l'chatchilah, one may recite it after chatzot. That is what I wrote above, since b’dieved everyone agrees that he fulfills his obligation. There is also concern that if one divides the recital of Birkot HaShachar, he will forget to recite a certain berachah afterwards.

^ 5.The Mishnah Berurah 47:30 writes that if the first time he wakes up is after chatzot, he may recite Birkot HaShachar. He did not specify whether it is preferable to recite them particularly after the first rising. However, the Kaf HaChaim 46:49 writes based on the Kabbalah, that it is best to recite them following the first waking after chatzot. One who cannot determine which rising is considered his main one should practice according to the Kaf HaChaim and recite them after the first rising.
Further, it is important to note that according to the Mishnah Berurah 47:30, the berachot, Elokai Neshamah and Hama’avir sheinah me’einai are to be recited after the first rising without Shem u’Malchut (Hashem's name), and the second time he recites them with Shem u’Malchut. However, if he recited them with Shem u’Malchut the first time, he may not go back and repeat them a second time. The Bei’ur Halachah expands on this, saying that according to the Pri Chadash they must be recited only after he finishes sleeping that night. If he recites them the first time he wakes up, he does not fulfill his obligation, and he must go back and recite them after the second time he wakes up. The Chayei Adam agrees with him concerning Hama’avir sheinah. However, Sha’arei Teshuvah and Derech HaChaim write not to repeat it after waking up the second time. Therefore, the Mishnah Berurah rules that if a person already recited them, he may not go back and say them again. Kaf HaChaim 46:49 writes in the name of a number of poskim and kabbalists that even these two berachot need to be recited the first time with Shem u’Malchut and any sleep after that is considered similar to a nap taken during the day. That is how Sephardim practice. The Ashkenazim follow the Mishnah Berurah, yet, even according to him, if they recited the blessing the first time, they fulfilled their obligation. In my humble opinion, it seems that it is better to teach both Ashkenazim and Sepharadim to recite all the berachot after the main waking, because when one recites most of the berachot with the first rising and leaves two berachot for the second rising, there is concern that he will make a mistake, either by forgetting to say the last two berachot, or by accidentally reciting all the berachot again the second time he wakes up. Therefore, I concluded above to recite all of Birkot HaShachar after the main waking and even when the first waking is the main one, a person who recites Elokai Neshamah and Hama’avir sheinah at that point has on whom to rely.
According to the kabbalists, the best time to recite Birkot HaShachar for one who was awake all night is after chatzot, and Birkot HaTorah after alot hashachar. However, the Ben Ish Chai, Toldot 14, writes concerning someone who goes to sleep after chatzot, that although according to the Rashash he may recite Birkot HaShachar after chatzot before he goes to sleep, the custom is to recite them after one wakes up, as Rav Eliyahu writes in his siddur, p. 3.
^ 6.The Sephardic minhag, based on the Ari, is explained in Kaf HaChaim 46:49. The Kaf HaChaim also writes that according to the Kabbalah, Birkot HaShachar should be recited immediately after chatzot; however, one must be careful to recite Birkot HaTorah only after alot hashachar. See further in this book, chapter 10, note 8.
The Mishnah Berurah 46:24 writes that according to the Eliyah Rabbah, one who did not sleep should not recite Elokai Neshamah and Hama’avir sheinah. The Pri Megadim and the Sha’arei Teshuvah indicate that this matter requires further study. The Sha’arei Teshuvah concludes that one should fulfill his obligation by hearing them recited from another person. This implies that if there is no one he can listen to recite the berachot he may not recite them due to doubt. Still, the Aruch HaShulchan 46:13 writes that according to the Rama one may recite the berachot. An Ashkenazi who follows that custom has on whom to rely (and perhaps in order to limit disagreement, the ruling should be according to them). Regarding Birkot HaTorah, see the laws of Birkot HaTorah further in this book 10:7, where the opinions and customs are clarified.