Is it obligatory to make up all missed prayers?
All praise is due to Allah, and peace and blessings be upon our master the Messenger of Allah ﷺ.
Making up missed prayers (qaḍāʾ) is a sharʿī obligation, established by the practice of the Prophet ﷺ himself — when the disbelievers preoccupied him on the Day of the Trench and he missed the ʿAṣr prayer, he made it up afterward. This is further affirmed by the ḥadīth: "Fulfil what you owe to Allah, for Allah is most deserving of being fulfilled." (Reported by al-Bukhārī.)
Accordingly, a person who has missed prayers should set aside his voluntary and Sunnah prayers and replace them with make-up prayers in their stead. There is no objection to making up one missed prayer alongside each obligatory prayer that is performed — praying the equivalent missed prayer together with each current obligatory prayer as a practical and manageable way of gradually clearing one's debt of missed prayers. And Allah the Almighty knows best.
What is the ruling on performing the standing (qiyām) and bowing (rukū‘) portions of the prayer normally, while performing the prostration (sujūd) seated due to knee pain?
All praise is due to Allah, and peace and blessings be upon our master, the Messenger of Allah ﷺ.
If performing sujūd (prostration) in prayer causes the worshipper pain in the knees, then it is permissible for him to perform it through gesture (īmā') while seated, since Allah, Glorified and Exalted is He, has lifted hardship from His servants. On the authority of ‘Imrān ibn Ḥuṣayn (raḍiyallāhu ‘anh), he said: "I suffered from hemorrhoids, so I asked the Prophet ﷺ about [how to perform] the prayer, and he said: 'Pray standing; if you are unable, then sitting; and if you are unable, then on your side.'" [Ṣaḥīḥ al-Bukhārī]
If the valid excuse later subsides, the worshipper is then obligated to perform the prayer with all its pillars and conditions fully observed — including standing, rukū‘ (bowing), and sujūd (prostration). 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.
Is Zakah (obligatory charity) due on the Zakah money received by a poor person, and reached a Nissab (minimum amount liable for Zakah), and a whole lunar year had lapsed over having it in his possession?
Yes, the poor who possessed a Nissab for a whole lunar year is obliged to pay the Zakah due on that money even if it was given to him as a Zakah money in the first place. And Allah Knows Best.