How many Rak`ahs (unit of prayer) are offered in Witr prayer?
All perfect praise be to Allah, The Lord of The Worlds Witr (an odd number prayer performed between Isha`a and Fajr) is offered with a minimum of one Rak`ah, and a maximum of eleven, but offering three Rak`ahs is the minimum of its complete form. And Allah Knows Best.
What is the ruling on performing istinja' before every ablution?
Istinja' is not from the conditions for the validity of ablution. It is only obligatory for prayer when there is impurity from urine or stool on the private part, or if there is fear of the impurity spreading to the body or clothing. And Allah the Almighty knows best.
When is Istikharah (guidance prayer) Du`a offered, before Tasleem (saying asalamu alikum warahmatu allah wa barakatuh to end the prayer), or after it?
It is offered after Tasleem.
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.