Does the clipping of nails nullify ablution?
No, it does not, and it is preferable to wash the hands afterwards.
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.
What is the ruling on water present on the floor of a toilet/bathroom?
The default ruling is the purity of this water present on the bathroom floor. If one is certain or strongly suspects its impurity, then one washes whatever part of the body or clothing this impure water has touched. If one doubts its impurity, the default is purity, and we do not rule it impure based on mere doubt. And Allah the Almighty knows best.
If a woman becomes pure from menstruation shortly after Fajr in Ramadan, what is required of her?
If a woman becomes pure (from menstrual period) after Fajr, even shortly after, it is recommended (but not obligatory) for her to refrain from eating and drinking for the rest of the day. However, she must make up for that day after Ramadan.
She will be rewarded for both refraining from eating (imsak) and making up the fast (qada) since she was menstruating for part of the day.