Should missed Sunnah prayer be made up?
Making up missed voluntary acts of worship is from Sunnah.
What should a person who doubted having missed a pillar of prayer do?
All praise be to Allah, The Lord of The Worlds. The prayer of one who doubts having missed one of its pillars is valid, and nothing is due on him/her since having a doubt after offering the act of worship doesn`t undermine its validity. And Allah 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.
How should I deal with the whispers of the devil with regard to ablution and purity?
Whispers in ablution are from the devil, and so you should take refuge in Allah from the devil`s evil suggestions that aim to distort the religion. Thus, once an organ is completely pure, don`t question its purity since having whispers doesn`t mean that the purity is invalid as it has already been established.