When is Istikharah (guidance prayer) Du`a offered, before Tasleem (saying asalamu alikum warahmatu allah wa barakatuh to end the prayer), or after it?
It is offered after Tasleem.
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 it permissible for the children of a deceased father to settle his debt from the Zakah (obligatory charity) money due on them?
It is impermissible to use the Zakah of one`s money for settling the debts of the deceased. However, children should settle the debts of their deceased parents out of filial piety. And Allah Knows Best.