What is "Shechem Echad" that Ya'akov gave to Yosef over his brothers?
Rashi #2, Rashbam and Seforno: He is referring to the Bechorah 3 (Yosef becoming two tribes) of which he spoke in the previous Pesukim.
Shechem, as well as meaning a portion, also hints at the city by that name.
And this is where he was buried, as the Pasuk in Yehoshua (24:32) relates. Also Targum Yonasan writes that Ya'akov gave Yosef Shechem as an extra portion, but he does not explain why. Hadar Zekenim - the Midrash says that since he was stolen from Shechem, his bones were returned to there. (Really, he was stolen in Dosan! Yakov had sent him to Shechem; perhaps he assumed that he was stolen there. Alternatively, Dosan is not a different place. Refer to 37:17:2:2* - PF)
Who gave Ya'akov a mandate to give Yosef an extra portion of the land that belonged to all his sons?
According to the Ramban, the division of Yosef into two tribes is equivalent with the Bechorah, that he bequeathed to Yosef, whereas the extra portion was a separate gift - all based on the great love he bore him. Moshav Zekenim - Bechorah [that Yakov bought from Esav] is Avodah. We do not find that Kehunah comes from Yosef! Kehunah should have been for the Bechoros, just after the Egel it was given to Levi. (How does this answer his question? Before the Egel, the Avodah was through any Bechor. It was not special to Yosef! - PF)
Moshav Zekenim, Riva (43:34) - there was no concern for jealousy, for it is proper to honor a king more. Da'as Zekenim - before they were jealous, for he was smaller than them. Now, they needed him.
Who is the Emori, from whom Ya'akov took the Bechorah?
Rashi: Eisav, who behaved like an Emori, or who would 'trap' his father with the words of his mouth (be'Imrei Piv).
Targum Yonasan: It is the residents of Shechem. 4
The first and the toughest of the seven nations, part of whom Menasheh captured in Ever ha'Yarden in the days of Moshe, and part, Yehoshua captured later and gave to Efrayim (See Ramban),
By which he meant Yehoshu'a (see Rashbam). Many Nevu'os are written in the past tense. (Hadar Zekenim 49:4, regarding a different matter).
What did he then mean when he added "with my sword and my bow"?
Rashi #1 and Seforno: He was referring to the wisdom and the Tefilos 1 via which he 'captured the Berachos from Eisav.
Rashi #2: Following the episode with Shechem, others gathered to fight against Yakov's family, and Yakov girded his weapons against them. 3
Ramban #2: Ya'akov stretched out his sword and shot arrows in the direction of the Emori, a sign that they would capture it. 4
Targum Yonasan: He was referring to the battle of Shechem. He took his weapons and assisted [his sons].
Hadar Zekenim: After they wiped out Shechem, Nochrim came to fight them. Yakov helped his sons against them. He proved to them that he is stronger than them, and the victory was primarily due to him.
The Seforno interprets "be'Kashti" as 'my understanding' ('be'Chochmasi u'Binasi') - which are the swords and bows of Tzadikim, as we find in Tehilim (45:4 [See Shabbos, 63a]) - See Seforno.
This hints to the Pasuk in Yehoshua (11:19-20), which informs us that, with the exception of the inhabitants of Giv'on opted to fight and were defeated.
Moshav Zekenim: Hashem put fear on the other nations, and they did not pursue Yakov! (35:5) Rather, they gathered in one city, so if Bnei Yakov come to attack them, they will fight with them.
רש"י: שאתה טורח...בקבורתי: למה יעקב לא אמר זאת ליוסף בשעה שביקש ממנו על הקבורה?
גור אריה: כאן בא לחלק את הארץ לשבטים ולכן נתן ליוסף את חלקו.
רש"י: חכמתו ותפלתו: למה החכמה חרב והתפילה קשת?
גור אריה: החכמה חריפה וחדה כחרב, והתפילה תלויה בלשון הנקראת חץ, ותפילת הצדיק עולה וקורעת עליונים ותחתונים כחץ מקשת. 1
עי' במהר"ל (נתיבות עולם, נתיב הלשון פ"א עמ' סד, ד"ה אמנם) שהלשון נקראת חץ כי היא לא דבר גשמי, והיא פועלת במהירות כמו חץ.
מה פירוש "חרבי וקשתי"?
גור אריה: לאונקלוס התפילה היא חרב כי היא קורעת עליונים ותחתונים, והתחינה היא קשת- כי כאשר מתקשה בתפילתו הוא מתחנן יותר.