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 it permissible for a person to sever ties with his sister because her husband had quit prayer and done him harm?
A sister is a blood-relative and maintaining blood-relations is obligatory in Islam. As regards her husband, he should be invited to the way of Allah with wisdom and beautiful preaching.
Is it permissible for a person who has to make up for missed fasts to fast six days of Shawwal (the month directly after Ramadan) before making up for the missed fasts?
Yes, it is permissible for him/her to do so, but it is better that they make up for missed fasts first. And Allah Knows Best.
Is it permissible to offer Tahajjud prayer after Witr prayer?
It is permissible to offer voluntary prayer after Witr (An odd number prayer performed between Isha and Fajr) prayer. However, it is desirable that the night prayer be ended with Witr. Therefore, it is desirable for one, who thought that he was most probably going to wake up at night in order to offer Tahajjud, to offer Witr after it, but one, who fears that he might not wake up, should offer Witr before going to bed.