What is the authenticity of the supplication: "O Allah, bring it upon us with blessings and faith, safety and Islam, and success in what You love and are pleased with. My Lord and your Lord is Allah"?
On the authority of Talhah Ibn Ubayd Allah (may Allah be pleased with him) who reported that the Prophet (PBUH) would say when he saw the crescent moon: "O Allah, let this moon appear over us with blessings and faith, safety and Islam. My Lord and your Lord is Allah."
This was narrated by Tirmidhi (Hadith no. 3451), who said: "It is a Hasan (good) Hadith."
And Allah The Almighty Knows Best.
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.
Is it permissible for a wife to refuse to go to bed with her husband (for sexual intercourse)?
It isn`t permissible for her to do so unless for a sound reason.
Is it permissible to offer Istikhara prayer (seeking guidance) after Witr Prayer (A confirmed Sunnah which is offered after Isha prayer and before Fajir prayer with a minimum of 3 Rak`as and a maximum of 11)?
It is permissible to offer Istikhara before and after Witr prayer as it is permissible at any time except that in which prayer is disliked. And Allah Knows Best.