How to perform the witr prayer in terms of connection (wasl) and separation (fasl)?
Praise be to Allah, and peace and blessings be upon our Master, the Messenger of Allah.
The Witr prayer has several forms that vary in terms of virtue:
The First Form: Separating every two units (rak‘ah) with a Tashahhud and a Taslim (salutation). This is superior to connecting the units, even if it is only a single rak‘ah. This is based on the Hadith of ‘Aishah (may Allah be pleased with her): 'The Messenger of Allah ﷺ used to pray eleven units between the end of the ‘Isha prayer and dawn, performing the Taslim after every two units and performing Witr with a single unit.' (Related by al-Bukhari & Muslim).
The Second Form: Connecting the units with only one final Tashahhud at the very end.
The Third Form: Connecting with two Tashahhuds—meaning reciting the Tashahhud before the final unit without performing the Taslim, then standing to complete the final unit. This form is considered the lowest in rank so that the Witr prayer remains distinct from the obligatory Maghrib prayer, as stated in the Hadith: 'Do not make the Witr resemble the Maghrib prayer.' (Narrated by Al-Daraqutni, who stated its narrators are trustworthy).
It is stated in Bushra al-Karim Sharh al-Muqaddimah al-Hadramiyyah: 'It is permissible to connect [the Witr] with one Tashahhud in the final unit—which is better—or with two Tashahhuds in the last two units, as both methods are established in Sahih Muslim from the actions of the Prophet ﷺ. In the connected method, more than two Tashahhuds are prohibited. Furthermore, separating (al-Fasl) is better than connecting (al-Wasl) if the number of units is the same, because the Hadiths supporting it are more numerous and it involves more devotional actions.' And Allah the Exalted knows best."
Is "Bismillāhir-Raḥmānir-Raḥīm" a verse (āyah) of Sūrat al-Fātiḥah?
All praise is due to Allah, and peace and blessings be upon our master, the Messenger of Allah ﷺ.
The basmalah ("Bismillāhir-Raḥmānir-Raḥīm") is, without question, a verse (āyah) of the Noble Qur'an, and according to the Shāfi‘ī school, it constitutes a verse of Sūrat al-Fātiḥah itself. Al-Fātiḥah is a pillar of the prayer, and it consists of seven verses, of which the basmalah is one. The prayer is not valid without reciting it, nor if any of the Fātiḥah's verses, letters, or shaddahs (consonant doublings) are omitted or altered.
It is stated in Bushrā al-Karīm (Vol.1/p.202), from the books of the Shāfi‘ī school: "The basmalah is a complete verse of it [i.e., of al-Fātiḥah] in practice — and it suffices, for this to be established, that there be strong probability (ẓann), especially given that this has come very close to certainty (yaqīn), due to the consensus (ijmā‘) of the Companions on its inclusion in the muṣ-ḥaf [the written text of the Qur'an] in its script, despite their extreme diligence in excluding from it anything that did not genuinely belong to it — to the point that they even [carefully regulated] its diacritical dots and vowel markings." And Allah, the Exalted, knows best.
Should missed Sunnah prayer be made up?
Making up missed voluntary acts of worship is from Sunnah.
What is required of one who doubts the number of rakʿāt during prayer?
All praise is due to Allah, and peace and blessings be upon our master the Messenger of Allah ﷺ.
If a person doubts the number of rakʿāt he has prayed, he should build upon the lesser number, as that is what he is certain of. He should then perform the prostration of forgetfulness (sujūd al-sahw) before the final salām at the end of the prayer. ʿAṭāʾ ibn Yasār narrated that the Messenger of Allah ﷺ said: "When any one of you is in doubt during his prayer and does not know whether he has prayed three rakʿāt or four, let him pray one more rakʿah and then perform two prostrations while seated before the salām. If the rakʿah he prayed was a fifth, these two prostrations will make it even; and if it was the fourth, then the two prostrations serve as a humiliation for the devil." (Reported by Abū Dāwūd.)
It is stated in al-Muqaddimah al-Ḥaḍramiyyah — one of the foundational texts of the Shāfiʿī school: "If one doubts whether he has prayed three rakʿāt or four, he is obliged to build upon the lesser number."
However, if such doubt recurs repeatedly and reaches the level of obsessive whispering (waswasah), he should not build upon the lesser number in that case — rather, he should build upon the greater number. And Allah the Almighty knows best.