Does the clipping of nails nullify ablution?
No, it does not, and it is preferable to wash the hands afterwards.
Is it permissible to make up missed prayers at the times in which praying is disliked?
All perfect praise be to Allah,The Lord of The Worlds It is permissible to make up missed prayers at any time even that in which praying is disliked. Absolute supererogatory prayer is forbidden to be performed at the times in which praying is disliked, and this also applies to Ihram and Istikhara prayers. However, there is no harm in offering prayers in Mekah during those times. And Allah Knows Best.
What is the ruling on swearing on the Holy Quran and breaking that oath?
It is impermissible to swear on the Holy Quran in vain, and it is also impermissible to subject it to such an act since breaking the oath after swearing on the Quran entails an expiation.
Is it permissible for a pious Muslim woman to stay with her husband who had quit praying out of laziness?
Quitting prayer is one of the major grave sins that come after disbelieving in Allah, but the wife of such a person isn`t considered divorced, rather, she should exert all her efforts in order to bring him back to the way of Islam. However, if his sin is likely to lure her from the way of Islam, then she had better separate from him by lawful means such as Mokhal`aa (When a wife pays a compensation for her husband in return for divorcing her). Moreover, if she exercises patience, and remains steadfast on her faith, then there is no harm in doing that.