Is it permissible for one to give the Zakah (obligatory charity) to his indebted brother?
It is permissible for one to give the Zakah to his brother if he was indebted, or poor.
Is a menstruating woman obliged to pray during menses, and should she make up missed prayers?
All perfect praise be to Allah, The Lord of The Worlds A menstruating woman is prohibited from prayer during her menses, and she isn`t obliged to make up missed prayers. And Allah Knows Best.
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 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."
