What is the recommended supplication (Du'a) upon breaking the fast, and is it recited before or after breaking it?
All praise is due to Allah, and peace and blessings be upon our master, the Messenger of Allah.
It is recommended (Mustahabb) for a fasting person to recite upon breaking the fast—that is, immediately after eating or drinking—the supplication: "Allahumma laka sumtu wa 'ala rizqika aftartu" (O Allah, for You I have fasted, and with Your provision I have broken my fast).
This is because our master, the Prophet (peace and blessings be upon him), used to say this. The narration was recorded by Abu Dawud with a good (Hasan) chain of transmission, albeit in a Mursal form (a narration where a Successor reports directly from the Prophet). Shaykh al-Islam Imam Ibn Hajar al-Haytami (may Allah have mercy upon him) stated: "Its Mursal status is inconsequential, as it pertains to virtuous deeds (Fada'il); furthermore, it was connected (Mawsul) through another chain of transmission." [Tuhfat al-Muhtaj, Vol.3/P.425]
It is also recommended to recite: "Dhahaba al-dhama'u wa ibtallat al-'uruqu wa thabata al-ajru in sha' Allah" (The thirst has gone, the veins are moistened, and the reward is confirmed, if Allah wills).
This was recorded by Abu Dawud with a good (Hasan) chain. Our leading jurists (Imams) have explicitly stated that it is recommended for the fasting person to combine both supplications.
Imam al-Bajuri (may Allah have mercy upon him) stated:
"And his saying following his breaking of the fast—that is, it is recommended to say: 'O Allah, for You I have fasted, upon Your provision I have broken my fast, in You I have believed, to You I have submitted, and upon You I have relied. The thirst has gone, the veins are moistened, and the reward is confirmed, if Allah wills. O You of vast bounty, forgive me. Praise be to Allah Who aided me so that I fasted, and provided for me so that I broke my fast. O Allah, grant us success in fasting, enable us to stand in night prayer during it, and aid us in it while people sleep, and admit us to Paradise in peace.'" [Hashiyat al-Bajuri, Vol.1/P.562]
Furthermore, the fasting person may supplicate with whatever good he or she wishes, for the supplication of a fasting person is answered. Al-Bayhaqi recorded on the authority of Anas ibn Malik that the Messenger of Allah (peace and blessings be upon him) said: "Three supplications are not rejected: the supplication of a parent for his child, the supplication of a fasting person, and the supplication of a traveler." And Allah 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.
What is the ruling on making up missed prayers during prohibited times?
Praise be to Allah, and peace and blessings be upon our Master, the Messenger of Allah.
It is permissible to make up (qada’) missed prayers at any time, even during the periods when prayer is generally prohibited. The prayers that are forbidden and considered invalid during these times are 'absolute voluntary prayers' (nafl mutlaq)—which have no specific cause—and voluntary prayers whose cause follows the prayer itself, such as the Sunnah of entering Ihram or the Sunnah of the Istikharah prayer. Furthermore, no prayer is considered disliked (makruh) during these prohibited times when performed within the Meccan Sanctuary (Makkah al-Mukarramah).
It is stated in Bushra al-Karim (Vol.1/P.181), one of the Shafi’i texts: 'It is not forbidden to perform prayers that have a cause that is not delayed (i.e., the cause is preceding), such as making up a missed prayer (fa’itah)—even if it was a voluntary one—and the funeral prayer (janazah); or a cause that is simultaneous, such as the prayer for rain (istisqa’) or the eclipse prayer (kusuf)... and the Sunnah of wudu, the greeting of the mosque (tahiyyat al-masjid), the Sunnah of circumambulation (tawaf), the Sunnah of arrival, and the prostrations of recitation (tilawah) or thankfulness (shukr). These mentioned prayers and their like are not forbidden provided that one does not specifically intend (ta'ammud) to perform them during the disliked time because it is a disliked time. If one does so intentionally, it becomes forbidden, even if it is a mandatory makeup prayer that is due immediately; because in that case, one is acting in defiance of the Sharia. This is in contrast to when one does not specifically seek out that time, even if the prayer happens to fall within it, or if one seeks it for another purpose—such as delaying a funeral prayer to that time so that a larger number of people may pray over the deceased; in such cases, it is permissible and valid... And it is forbidden to perform prayers with no cause at all, like absolute nafl, or those with a delayed cause, such as the Istikharah prayer, the prayer for Ihram, the prayer for a need (hajah), the prayer before leaving the house, or the prayer before execution; because their causes occur after the prayer itself.' And Allah the Exalted knows best."
Is it permissible to pay the Fitr Zakah (obligatory charity) of Ramadan on behalf of a dead person?
The Fitr Zakah of Ramadhaan isn`t due on one who had passed away before the sunset of the last day of Ramadan. And Allah Knows Best.