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.
Someone wiped over his shoes after wearing them in a state of purity, then took them off and prayed without them?
Ablution is not invalidated by taking off leather socks or shoes after wiping over them. However, whoever takes them off after wiping must wash his feet only. If he prayed without washing his feet, he must wash his feet and repeat the prayer. And Allah the Almighty knows best.
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.
How many Rak`ahs (unit of prayer) are offered in Witr prayer?
All perfect praise be to Allah, The Lord of The Worlds Witr (an odd number prayer performed between Isha`a and Fajr) is offered with a minimum of one Rak`ah, and a maximum of eleven, but offering three Rak`ahs is the minimum of its complete form. And Allah Knows Best.