Does the clipping of nails nullify ablution?
No, it does not, and it is preferable to wash the hands afterwards.
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 have an intention (niyyah) for every prayer?
Praise be to Allah, and peace and blessings be upon our Master, the Messenger of Allah.
It is obligatory for the worshiper to have a specific intention (Niyyah) for every prayer, meaning they must consciously intend the act of worship they are performing. The intention is a pillar (Rukn) of the prayer, and the prayer is not valid without it. It is not a requirement to utter the intention verbally; rather, doing so is considered a recommended Sunnah. And Allah the Exalted 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.