Is a menstruating woman obliged to pray during menses, and should she make up missed prayers?

All perfect praise be to Allah, The Lord of The Worlds                                                                                                                                                                        A menstruating woman is prohibited from prayer during her menses, and she isn`t obliged to make up missed prayers. And Allah Knows Best.

How do I deal with whispers (waswasa) in ablution and purification?

Whispers in ablution are from Satan, and the Muslim should not pay attention to them. He is not required to re-perform ablution or repeat washing a limb because of waswasa. He should always base his purification on its being valid. It is recommended for him to frequently say "La ilaha illa Allah" (There is no god but Allah), because Satan recoils when Allah is mentioned. And Allah the Almighty knows best.

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.

Does tooth extraction during the day in Ramadan break the fast?