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.
Is it permissible to offer mandatory prayer while sitting?
All perfect praise be to Allah, The Lord of The Worlds, and may His Peace and Blessings be upon our Prophet Muhammad and upon all of his family and companions. Standing up is a pillar in the mandatory prayer and the prayer is not valid without it unless one cannot do it. As for Nafila (supererogatory prayer), one can perform it in the state of sitting even if he/she can stand, but his/her reward is half the reward of the person who prays while standing if he/sh has no legal excuse for such an act. And Allah Knows Best.
Is the two Raka's after Friday Prayer an act of Sunna?
Performing Two prostrations after the call of Friday's Athan is an act of Sunna, since Al-Bukhari stated in his Sahih: (The chapter of praying before and after Friday's prayer). This indicates that he mentions Friday's prayer exactly as the Duhr prayer (Afternoon prayer) as regards praying before and after the call of Athan. And Allah Knows Best.
Does the clipping of nails nullify ablution?
No, it does not, and it is preferable to wash the hands afterwards.