Is supplicating in Qunoot, at times of affliction, during obligatory and voluntary prayer a Sunnah, and should it be done before Rukoo` (bowing), or after it?
At times of affliction, it is a Sunnah that Muslims supplicate in Qunoot after the final Rukoo` of each obligatory, or voluntary prayer as individuals, or in congregation.
What is the ruling on istinja' after urination, and is it done with water and soap or with water only?
Istinja' from urine and stool is obligatory. It is permissible to perform istinja' with water alone, or with toilet paper alone. The best way is with toilet paper then water. If one wishes to suffice with one of them, then water is better. And Allah the Almighty knows best.
What is the ruling on discharges two or three days before the expected period of menstruation and the light-colored blood accompanying it? Must the woman abstain from prayer during this period?
If the total duration of these blood-tinged discharges reaches a day and a night (24 hours) or more, it is considered menstruation. If their total does not exceed 24 hours, it is not considered menstruation but is irregular bleeding (dam al-fasad). Each woman has specific cases for which she should ask the scholars. And Allah the Almighty knows best.
What is the ruling on reciting the takbīr from Sūrat aḍ-Ḍuḥā to Sūrat an-Nās upon completing the recitation of the Qur'an (khatm)?
All praise is due to Allah, and peace and blessings be upon our master, the Messenger of Allah ﷺ.
It is recommended to recite the takbīr from the beginning of Sūrat aḍ-Ḍuḥā through to the end of Sūrat an-Nās, and this is the recitation practice of the people of Makkah.
It is stated in Nihāyat az-Zayn (p. 65): "It is sunnah to begin each sūrah with the basmalah, since it constitutes a verse of it. It is also sunnah to say, before each sūrah — from aḍ-Ḍuḥā to the end of the Qur'an — 'Lā ilāha illallāh, wallāhu akbar' (There is no god but Allah, and Allah is the Greatest), based on what has been narrated regarding Imam ash-Shāfi‘ī (raḍiyallāhu ‘anh), who heard a man reciting this takbīr in prayer, and said to him: 'You have done well, and you have hit upon the sunnah.'"
And Allah, the Exalted, knows best.