Al-jawab billahi at-taufeeq (the answer with Allah's guidance)
1) Three Rakats only, according to Imam Abu Hanifah (Rahmatullahi Alaih):
It is reported from Sayyiduna Hasan al-Basri that there was general agreement of the early generations (Salaf) that Witr is 3 Rakats [this was reported by Ibn Abi Shayba in his Musannaf and by Imam Tahawi], and the great Faqih (jurist) of the Companions of the Prophet (Sallallaha Alaihi Wasallam), Abdullah ibn Mas`ud (RadhiyAllahu Anhu), said, “Witr is 3 rakats, like the Rakats of Maghrib,” and he said, “One Rakat does not fulfill it.”
(Zayla`i, Tabyin al-Haqa’iq Sharh Kanz al-Daqa’iq, Nasb al-Raya)
It is agreed that there is no such thing as a one-Rakat prayer. You cannot, for example, pray 1 rakat Nafl for Allah.
Aisha (RadhiyAllahu Anha) narrates that Rasulullah (Sallallahu Alaihi Wasallam) did not make Salam after the first two Rakat of the Witr Salah.
Reported by Hakim (Mustadrak Vol.1 Pg.304). He classified it as Sahih according to the conditions of Imam Bukhari and Imam Muslim (Rahmatullahi Alaihima). Hafiz Zahabi (Rahmatullahi Alaih) also agreed with him.
2) To recite Dua Qunut before Ruku:
I asked Anas bin Malik (RadhiyAllahu Anhu) about the Qunut. Anas (RadhiyAllahu Anhu) replied, "Definitely it was (recited)". I asked, "Before bowing or after it?" Anas (RadhiyAllahu Anhu) replied, "Before bowing." I added, "So and so has told me that you had informed him that it had been after bowing." Anas (RadhiyAllahu Anhu) said, "He told an untruth (i.e. "was mistaken," according to the Hijazi dialect). Allah's Apostle recited Qunut after bowing for a period of one month." Anas added, "The Prophet (Salallahu Alaihi Wasallam) sent about seventy men (who knew the Quran by heart) towards the pagans (of Najd) who were less than they in number and there was a peace treaty between them and Allah's Apostles (but the Pagans broke the treaty and killed the seventy men). So Allah's Apostle recited Qunut for a period of one month asking Allah to punish them." (referring to the Qunutun Naazilah) (Bukhari, Volume 2, Book 16, Number 116)
Allaama Ibn Hajar (Rahmatullahi Alaih) writes in his commentary on Bukhari, Fath al-Bari that after analysing all these narrations we learn that it was the normal practice to recite the Qunut before Ruku.
However, on certain occasions (such as the befalling of a calamity, etc.) the Qunut would be recited after Ruku. (vol. 1, pg. 291)
In Musannaf Ibn Abi Shaybah it is mentioned that for this very reason the Sahaaba-e-Kiraam (RadhiyAllahu Anhum) used to recite the Qunut before Ruku.
Asim Ahwal narrates: :I asked Anas (RadhiyAllahu Anhu) concerning Qunut (can we read it?)". Anas (RadhiyAllahu Anhu) replied in the affirmative. I then inquired;"Is it before Ruku' or after Ruku'?" Anas (RadhiyAllahu Anhu) replied: Before Ruku'." (Bukhari Vol.2 Pg.587)
Abdul Aziz states: "I asked Anas (RadhiyAllahu Anhu) about Qunut, whether it is to be recited after Ruku' or upon completing the Qira'ah?" Anas replied: "Nay, but after completing the Qira'ah." (Bukhari Vol.2 Pg.586)
(See also: I`laus Sunan Vol.6 Pg. 68, Tahaawi Vol.1 Pg.122 and Ahsanul Fataawa Vol.3 Pg.495)
Praying Witr behind a Shaf'i Imam:
If the Shaf'i Imam prays Taraweeh with two Salams then this will not be valid according to the Hanafis. If he does not do this then it will be valid. (Bahrur Raiq Vol.2 Pg.39,40, Durrul Mukhtar Vol.2 Pg.7,8)
Also, In the situation when the Shafi`i Imam recites his Qunut (which is after the Ruku'), it will be necessary to follow him in this situation and recite Du'a Al-Istia'nah (Du'a Qunut) and not Du'a Al-Hidayah (Qunut An-Nazilah). (Shami Vol.1 Pg. 626)
3) The Du'a Qunut should be recited silently:
Allah Ta'ala says,
“Call on your lord with humility and in private” (al-A’raf, 55).
Please refer to this also: http://www.muftisays.com/qa.php?viewpage=viewQA&question=1518http://www.muftisays.com/qa/question/873/sallatulwitr.html
And Only Allah Ta'ala Knows Best.